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#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | psi4/psi4 | psi4/driver/procrouting/proc.py | Python | lgpl-3.0 | 203,989 | [
"Psi4"
] | fc32899d9aa2f128f3f81d746496c93de54acb4553c73bbeeaaefc71ff58698a |
# NOTE: This example uses the next generation Twilio helper library - for more
# information on how to download and install this version, visit
# https://www.twilio.com/docs/libraries/python
import os
from twilio.rest import Client
# Your Account Sid and Auth Token from twilio.com/user/account
# To set up environmenta... | TwilioDevEd/api-snippets | notifications/rest/credentials/list-credential/list-credential.7.x.py | Python | mit | 590 | [
"VisIt"
] | 1ae7504e8f8a4d4d51b9ab268a946d86e4233437cf35fff73db734abab97fb7e |
#!/usr/bin/env python
#
# Wrapper script for starting the biopet-vcffilter JAR package
#
# This script is written for use with the Conda package manager and is copied
# from the peptide-shaker wrapper. Only the parameters are changed.
# (https://github.com/bioconda/bioconda-recipes/blob/master/recipes/peptide-shaker/pe... | joachimwolff/bioconda-recipes | recipes/biopet-vcffilter/biopet-vcffilter.py | Python | mit | 3,369 | [
"Bioconda"
] | 4adf52ae1bcfa74ef3f916035fc4caee619f3c98cddd06ddeeb28d358553e4d7 |
"""
This class brings together a L{solve.Solver} to choose a set of implmentations, a
L{fetch.Fetcher} to download additional components, and the user's configuration
settings.
@since: 0.53
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall impor... | rammstein/0install | zeroinstall/injector/driver.py | Python | lgpl-2.1 | 7,097 | [
"VisIt"
] | 386f635793f363f634c6d31939dd1be852812c94036b7f5e4516c73aa43a81b0 |
# https://flashair-developers.com/en/documents/api/
from __future__ import unicode_literals, print_function
import attr
from attr.validators import and_, instance_of
from constantly import FlagConstant, Flags
from twisted.python.url import URL
from twisted.python.filepath import FilePath
from twisted.internet.defe... | exarkun/txflashair | src/txflashair/txflashair.py | Python | mit | 5,107 | [
"VisIt"
] | 61757556d1cb02cce82357f84dbfce30b99a3fc852f8f33571006c93eddb5c9d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright 2010 British Broadcasting Corporation and Kamaelia Contributors(1)
#
# (1) Kamaelia Contributors are listed in the AUTHORS file and at
# http://www.kamaelia.org/AUTHORS - please extend this file,
# not this notice.
#
# Licensed under the Apache License... | sparkslabs/kamaelia_ | Sketches/MH/pixformatConversion/PixFormatConversion.py | Python | apache-2.0 | 10,021 | [
"DIRAC"
] | c680b69065521ec381a60ef002ec2cc2645243d22f0b80bdc782159068781e1c |
"""Classes for handling parameters and dictionaries of default values."""
# Fitting Hyper parameters:
# Time window for steady-state averaging
# IPI curve initial parameters
# fV initial parameters
# Kinetics initial parameters
# Optimisation routine initial parameters
# ...
from __future__ import print_function, div... | ProjectPyRhO/PyRhO | pyrho/parameters.py | Python | bsd-3-clause | 36,387 | [
"Brian",
"NEURON"
] | d15030973c267ee2c810bcaeef3bf0eec1f8605d00e9cfda67249d51983f788c |
"""For backward compatibility only, pulls app_factor from galaxy.webapps.main"""
from galaxy.webapps.galaxy.buildapp import app_factory
| mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/web/buildapp.py | Python | gpl-3.0 | 137 | [
"Galaxy"
] | 4f2427a617dc30ad2d1e07ed36d6898031144e13455194c1a70bf43a4438ed9b |
"""
PyArchiver Compression and Archiving Library
@author: Clivern U{hello@clivern.com}
"""
from __future__ import print_function
import os
import bz2
import gzip
import tarfile
class TarPack(object):
""" Read and Write TAR files """
def __init__(self, file, mode = 'r'):
"""
Init class instance
:param fil... | Clivern/PyArchiver | pyarchiver/tarpack.py | Python | mit | 4,216 | [
"VisIt"
] | 510fce07a09f40d64083fb18760d7c0ccb3db971e820b8f0049f53f6dac91394 |
# ! /usr/bin/python2
# -*- coding: utf-8; -*-
#
# (c) 2013 booya (http://booya.at)
#
# This file is part of the OpenGlider project.
#
# OpenGlider 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... | hiaselhans/OpenGlider | openglider/graphics/__init__.py | Python | gpl-3.0 | 6,340 | [
"VTK"
] | b3689156b0c3ca3102d1efe463495b39e491035fc5a406ee4cc9da622f0e0a6f |
import unittest, time, sys
sys.path.extend(['.','..','py'])
import h2o, h2o_cmd, h2o_glm, h2o_util, h2o_hosts, h2o_import as h2i
class Basic(unittest.TestCase):
def tearDown(self):
h2o.check_sandbox_for_errors()
@classmethod
def setUpClass(cls):
global localhost
localhost = h2o.dec... | woobe/h2o | py/testdir_single_jvm/test_GLM2_umass.py | Python | apache-2.0 | 2,634 | [
"Gaussian"
] | d4ca89d36d4dfe3eb20e649082153fed8c8428e982ba088e62604b4431382151 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Kyle A. Beauchamp
# Contributors:
#
# MDTraj is free software:... | kyleabeauchamp/mdtraj | mdtraj/tests/test_mol2.py | Python | lgpl-2.1 | 4,725 | [
"MDTraj"
] | 1f747eeb731223377151237b55db14e7040f6c39eb72a34f28608a11e66ceee1 |
#!/usr/bin/env python3
#title : core.py
#description : Core methods for distributions.
#author : Enys Mones
#date : 2015.06.19
#version : 0.1
#usage : python core.py
#========================================================
import numpy as np
from scipy import stats
from mp... | synesenom/model.py | core/core.py | Python | mit | 6,649 | [
"DIRAC",
"Gaussian"
] | 730354c449b6ed4aacda3e746564ddc03d6cd9d0324ac4a7c260ccee482c4457 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
""" pytest test configures """
import pytest
import os.path as osp
import numpy as np
import sisl
pytestmark = [pytes... | zerothi/sisl | sisl/io/siesta/tests/test_dm.py | Python | mpl-2.0 | 3,454 | [
"SIESTA"
] | c212d2df9bc30e8930556530738ed6005fa121d3f4dd1477c4ae81ad2979c49e |
import requests
import bs4
import json
from pymongo import MongoClient
from pymongo.errors import DuplicateKeyError, CollectionInvalid
import datetime as dt
# Define the MongoDB database and table
db_cilent = MongoClient()
db = db_cilent['zoeshrm']
table = db['Restaurant']
# Query the Yelp API once
def single_query(l... | kennethcc2005/travel_with_friends | restaurant_mongo.py | Python | mit | 4,820 | [
"VisIt"
] | 62d760a192ccc2d6b848e3cdd8d409186efce2297e7ad22745c5d183f117f367 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | sam-m888/gramps | gramps/plugins/tool/eventnames.py | Python | gpl-2.0 | 6,530 | [
"Brian"
] | e2aa9a86b8939eb16e419904a606b09772de2d7edd6f3025fb6cdf54bec2bdd7 |
import k3d
import pathlib
import vtk
path = pathlib.Path(__file__).parent.resolve()
def generate():
plot = k3d.plot(screenshot_scale=1.0)
model_matrix = (
1.0, 0.0, 0.0, 0.0,
0.0, 0.0, 1.0, 0.0,
0.0, 1.0, 0.0, 0.0,
0.0, 0.0, 0.0, 1.0
)
reader = vtk.vtkXMLPolyDataRead... | K3D-tools/K3D-jupyter | docs/source/showcase/VTK_polydata_plot.py | Python | mit | 608 | [
"VTK"
] | bd128237b0edc773bfdcdd5a1aca6ad9827329b489dae8952d11ee6aaf61ca70 |
"""
ConfigParser subclass for config files
with no sections.
"""
from distutils.core import setup
import setuptools # this import is needed so that some options and commands work
setup(
name='simple-configparser',
version='0.1.3.0',
author='Brian E. Peterson',
author_email='bepetersondev@gmail.com',... | bepetersn/simple-configparser | setup.py | Python | mit | 510 | [
"Brian"
] | a026f4753a9b0c602950c87f3149b5c5e67a89d32078b2aff14ad8daf2244a8a |
#
# 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... | pkreissl/espresso | testsuite/python/widom_insertion.py | Python | gpl-3.0 | 4,515 | [
"ESPResSo"
] | d997013653722dc5dd92bdd66e4d5488cffb80a6f511ab1b2cd3210991186ebc |
"""
=====================
CollectionViewer demo
=====================
Demo of CollectionViewer for viewing collections of images. This demo uses
the different layers of the gaussian pyramid as image collection.
You can scroll through images with the slider, or you can interact with the
viewer using your keyboard:
le... | chintak/scikit-image | viewer_examples/viewers/collection_viewer.py | Python | bsd-3-clause | 795 | [
"Gaussian"
] | 76be2394d70196dbc544d58d652989dd10e0f547337cf101e60d64b49885d552 |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/pbc/cc/kccsd_uhf.py | Python | apache-2.0 | 59,676 | [
"PySCF"
] | b9495332fd71d2836bfb16e63e5afcaf94b5208c6d9f54f2bb4f934d3631afee |
#!/usr/bin/env python3
########################################################################
# Solves problem 28 from projectEuler.net.
# Finds the sum of the diagonal in an spiral.
# Copyright (C) 2010 Santiago Alessandri
#
# This program is free software: you can redistribute it and/or modify
# it unde... | sanSS/programming-contests | project-euler/problem028.py | Python | gpl-3.0 | 1,254 | [
"VisIt"
] | 74465ad4c826741ce3d447237db57fc10ab6f94f9a2cd3d601ee4b04eb3c9991 |
#!/usr/bin/env python -i
# preceding line should have path for Python on your machine
# vizplotgui_gl.py
# Purpose: viz running LAMMPS simulation via GL tool with plot and GUI
# Syntax: vizplotgui_gl.py in.lammps Nfreq compute-ID
# in.lammps = LAMMPS input script
# Nfreq = plot data point and viz sh... | jag1g13/lammps | python/examples/vizplotgui_gl.py | Python | gpl-2.0 | 4,502 | [
"LAMMPS"
] | 5076709dcd118aadf6ad0688925da154fc68723b0d789e8e22c3cefd44e739c3 |
# Copyright 2005-2008 by Frank Kauff & Cymon J. Cox. 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.
#
# Nodes.py
#
# Provides functionality of a linked list.
# Each node has one ... | bryback/quickseq | genescript/Bio/Nexus/Nodes.py | Python | mit | 5,775 | [
"Biopython"
] | 545911f36af7b0da9704c7f66ffdee9f59bfc0de899128ecf3dd1035ef6d1774 |
"""
Define common steps for instructor dashboard acceptance tests.
"""
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
from __future__ import absolute_import
from lettuce import world, step
from mock import patch
from nose.tools import assert_in
from courseware.tests.factories import Staf... | solashirai/edx-platform | lms/djangoapps/instructor/features/common.py | Python | agpl-3.0 | 4,561 | [
"VisIt"
] | a826ae49e75603d8e85c7a306e1af6b6df01f9953490042027db5995b1d98538 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | src/pylada/vasp/nlep/systems.py | Python | gpl-3.0 | 8,872 | [
"CRYSTAL",
"VASP"
] | 2ebea03bd49f1da1ac69ede34fce071d92134bb4698b948bcc4dc2d79325decf |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2019 Jonathan Dent, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# ... | appleseedhq/blenderseed | translators/scene.py | Python | mit | 42,867 | [
"VisIt"
] | 95e97391f6e4b21cc6a0fd8a1453cd377ab77ab9fdaaad6d522bd909193cf57f |
# Copyright (c) 2014, Alexander Korobeynikov
# https://github.com/alveko/easymock
# License: BSD
import os, re, sys
from collections import namedtuple
sys.path.extend(['/ericsson/tools/pycparser'])
from pycparser import c_parser, c_ast, parse_file, c_generator
FuncDecl = namedtuple('FuncDecl',
... | alveko/easymock | gen/funcdecl.py | Python | bsd-3-clause | 8,048 | [
"VisIt"
] | d21efe8423586ab981c88d06b5151b2ff4de608d89ac98291d739b195d0a3207 |
import getroot
import sys
# LO cross sections from http://cms.cern.ch/iCMS/jsp/mcprod/admin/requestmanagement.jsp
# NNLO cross sections from https://twiki.cern.ch/twiki/bin/viewauth/CMS/StandardModelCrossSectionsat8TeV
datasets = {
'DYJets': {
'name': "DYJets",
'file': "madgraphSummer12",
'xsec': 2950.0,
'nl... | dhaitz/CalibFW | plotting/modules/background.py | Python | gpl-2.0 | 6,060 | [
"FEFF"
] | fe6bafe4694181b34a30b534ce694dc6d63b032443f1cc499af40ec54b1a45fd |
#!/usr/bin/python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Convert SVN based DEPS into .DEPS.git for use with NewGit."""
import optparse
import os
import sys
import deps_utils
import git_to... | windyuuy/opera | chromium/src/tools/deps2git/deps2git.py | Python | bsd-3-clause | 8,156 | [
"VisIt"
] | 9520eab633b42d8ffb4c965d96e9202d362537dc6cd51bea21b0ca48c703a1ff |
""" Comprehension patterns transforms list comprehension into intrinsics. """
from pythran.analyses import OptimizableComprehension
from pythran.passmanager import Transformation
from pythran.transformations.normalize_tuples import ConvertToTuple
from pythran.conversion import mangle
from pythran.utils import attr_t... | pombredanne/pythran | pythran/optimizations/comprehension_patterns.py | Python | bsd-3-clause | 5,680 | [
"VisIt"
] | 8252f163bfdc71c42fbad7239b116be39fc637605000be0f76b8365ac7b9e8dc |
from direct.showbase.PythonUtil import randFloat, normalDistrib, Enum
from direct.showbase.PythonUtil import clampScalar
from toontown.toonbase import TTLocalizer, ToontownGlobals
import random, copy
TraitDivisor = 10000
def getTraitNames():
if not hasattr(PetTraits, 'TraitNames'):
traitNames = []
... | Spiderlover/Toontown | toontown/pets/PetTraits.py | Python | mit | 9,550 | [
"Gaussian"
] | 7714c8fa423b6c5a93d0cd96736187d528064e62e0a6568406a3bc762384df7f |
"""Create HDF5 dataset for UCF-101.
Author: Yuhuang Hu
Email : duguyue100@gmail.com
"""
import os
import cPickle as pickle
import h5py
from spikefuel import dataset
def printname(name):
"""print name."""
print name
# paths
db_name = "UCF50_30fps_20160409"
save_path = "/home/inilab/data"
ucf50_data_path = "... | duguyue100/spikefuel | scripts/create_ucf50_dataset.py | Python | mit | 855 | [
"VisIt"
] | 5bf0c51e747b33b39c7b9028e331b0e8500bf4b22568851ff16eae8a9034a82b |
import smbl
import snakemake
import os
from ._program import *
BWA = os.path.join(smbl.bin_dir,"bwa")
##########################################
##########################################
class Bwa(Program):
@classmethod
def get_installation_files(cls):
return [BWA]
@classmethod
def su... | karel-brinda/smbl | smbl/prog/plugins/bwa.py | Python | mit | 3,737 | [
"BWA"
] | 314d59d68b49e18eeba976c0b7b6ad72f4cee06a6f9b0c3751af60ec9b141bae |
"""
Mesh generator class. Generates Zinc meshes using scaffoldmaker.
"""
from __future__ import division
import copy
import os
import math
import string
from opencmiss.maths.vectorops import axis_angle_to_rotation_matrix, euler_to_rotation_matrix, matrix_mult, rotation_matrix_to_euler
from opencmiss.utils.zinc.field ... | rchristie/mapclientplugins.meshgeneratorstep | mapclientplugins/meshgeneratorstep/model/meshgeneratormodel.py | Python | apache-2.0 | 65,320 | [
"VTK"
] | da3668ca4dfed350d7d2107b1bcd620e1687c184188c7de6d95c5e669ef83d43 |
import re
from tornado.escape import json_decode
from authlib.common.encoding import to_unicode
from authlib.oauth2 import OAuth2Request as _OAuth2Request
from authlib.oauth2.rfc6749.util import scope_to_list
from urllib.parse import quote
class OAuth2Request(_OAuth2Request):
"""OAuth2 request object"""
def... | DIRACGrid/DIRAC | src/DIRAC/FrameworkSystem/private/authorization/utils/Requests.py | Python | gpl-3.0 | 3,349 | [
"DIRAC"
] | d3b0c1198ddb32e2c5db87b9c6634b16062e80d277b35ee35023fe9a730dddfd |
#!/usr/bin/env python
from pyDFTutils.vasp.myvasp import myvasp, default_pps
from pyDFTutils.vasp.vasp_utils import read_efermi
from pyDFTutils.ase_utils.geometry import gen_disped_atoms
from ase.io import read
from pyDFTutils.wannier90.wannier import wannier_input,run_wannier
import os
def calc():
atoms = read(... | mailhexu/pyDFTutils | examples/wannier_vasp/BEC_BBB.py | Python | lgpl-3.0 | 2,069 | [
"ASE",
"VASP",
"Wannier90"
] | f492fe9e8c33b3c53b17862727ddedfc632509b517595b56b3cd593ed7c1fc91 |
"""
SpringLayout.py
This algorithm is based on the physical spring model, in the sense that nodes
with a link between them will want to pull each other together until the
distance between them equals the resting length of the 'spring'. The further
apart they are, the more force that is applied to bring t... | Balannen/LSMASOMM | atom3/Kernel/Layout/SpringLayout.py | Python | gpl-3.0 | 20,022 | [
"BLAST"
] | a0df4fec22ee2cc2eff233307a768e59188adbca004e70e550e242d714f31c57 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright 2010 C Sommer, C Straehle, U Koethe, FA Hamprecht. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without modification, are
# permitted provided that the following conditions are met:
#
# 1. Redistributions of... | ilastik/ilastik-0.5 | ilastik/modules/classification/core/features/standardFeatures.py | Python | bsd-2-clause | 12,940 | [
"Gaussian"
] | 62ac36d84de6106c12875c30d3840dac121ab043f12a324e3bb0c7721445e15d |
import warnings
import sys
import scipy
try:
import mayavi.mlab as mlab
import tvtk.api
from tvtk.util.ctf import PiecewiseFunction
except ImportError:
warnings.warn("mayavi and tvtk modules could not be loaded"
"mayavi plotting is unavailable")
def plotLine(vector,val=1.0, close=Fa... | icfaust/TRIPPy | TRIPPy/plot/mayaplot.py | Python | mit | 9,720 | [
"Mayavi"
] | 3e7aef0ceb78ebea98f571543ccc2945cd532b24d65e0d624841c633c63e1a9d |
"""Classes and methods for segmentation of spherical objects within cells."""
# IMPORT DEPENDENCIES
import matplotlib
import os
import sys
import pickle
import time
from operator import itemgetter
import numpy as np
import pandas as pd
from skimage import io
from skimage.morphology import watershed
from skimage.featu... | nrweir/pyto_segmenter | PexSegment.py | Python | gpl-3.0 | 45,265 | [
"Gaussian"
] | f919a0d16ad36086ea1c30a970e970cf1a9c530813f694993389c9683d6e23e4 |
"""
This module and its submodules contains utilities for running external
processes and interfacing with job managers. This module should contain
functionality shared between Galaxy and the Pulsar.
"""
from galaxy.util.bunch import Bunch
from .kill import kill_pid
__all__ = ('kill_pid', 'Bunch')
| galaxyproject/pulsar | pulsar/managers/util/__init__.py | Python | apache-2.0 | 299 | [
"Galaxy"
] | 532710d3c186285b2c2892d12064c45cd7463dec15f6459a34b572cfa7f86b50 |
"""
Creates all figures given directory of AIS-MCMC result csvs
"""
import matplotlib
import matplotlib.pyplot as plt; plt.ion()
import seaborn as sns
import pandas as pd
import numpy as np
import os, argparse, pyprind
# set global default font sizes
fontsize = 16
matplotlib.rcParams['xtick.labelsize'] = fontsize-3
ma... | jeff-regier/Celeste.jl | experiments/mcmc_scripts/make_mcmc_results_figures.py | Python | mit | 25,522 | [
"Galaxy"
] | a909ee712a15fe522c355e409ec517764db49d4e7fcfc00571b98cd444c79646 |
import Scientific
assert [int(x) for x in Scientific.__version__.split('.')] >= [2, 8]
from ase.calculators.jacapo.jacapo import *
| grhawk/ASE | tools/ase/calculators/jacapo/__init__.py | Python | gpl-2.0 | 131 | [
"ASE"
] | 1641e1989e073c5d28747fdd9f40f0acf22423eb94962ac67d8f25932750a90b |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
=========================================================
Principal components analysis (PCA)
=========================================================
These figures aid in illustrating how a point cloud
can be very flat in one direction--which is where PCA
comes in to ch... | pdedumast/ShapeVariationAnalyzer | src/py/fitlib/condyle_pca_decomposition.py | Python | apache-2.0 | 5,219 | [
"VTK"
] | 1eca12b2e6c9a541029dcbd8477635bf0266e44f0b4238d8da16528ceb7e012e |
# -*- coding: utf-8 -*-
# pylama:skip=1
r"""
Some information and hints about logs and log formats.
Logs analysis: https://www.wikiwand.com/en/Log_analysis
Make use of database models to avoid parsing logs again and again.
Also think to log rotation and archiving.
Real-time/past analysis:
- Number of visits and... | Pawamoy/django-meerkat | src/meerkat/logs/__init__.py | Python | isc | 22,069 | [
"VisIt"
] | 57f134dcf831e5560388d52ac8b88977e9746712ded6317f5484193296dc0838 |
import os, sys
sys.path.append(os.path.join(os.path.dirname(__file__)))
'''
added head source directory in path for import from any location and relative testing and pwd for open() relative files
'''
import time
import socket
from datetime import datetime as dtdt
from datetime import date as dtd
from dateutil.relativ... | toadkicker/elk-stack | extra/billing/tools/tools.py | Python | apache-2.0 | 10,856 | [
"Elk"
] | bb8d5087d25b691d36f255be9f3e689b3665a870ae30dee012ac2aec125f9e93 |
#
# 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/zoo/orca/learn/spark_estimator.py | Python | apache-2.0 | 7,286 | [
"ORCA"
] | b8e2405631b438eefc9e2f201877a6ba91787f6d7149327e735d85e57851fcb9 |
import ast
import gast
def _generate_translators(to):
class Translator(ast.NodeTransformer):
def _visit(self, node):
if isinstance(node, ast.AST):
return self.visit(node)
elif isinstance(node, list):
return [self._visit(n) for n in node]
... | serge-sans-paille/gast | gast/astn.py | Python | bsd-3-clause | 1,057 | [
"VisIt"
] | b9cae02fc38c1807d65693f05543954c0d9c91295313cdc3ebb514d2ba7de10e |
#!/usr/bin/env python
from __future__ import division
from __future__ import print_function
import argparse
import numpy as np
import pandas as pd
import sys
import os
import matplotlib as mpl
#mpl.use('Agg')
import matplotlib.pyplot as plt
import matplotlib.colors as colors
import matplotlib.dates as md
from matplot... | meteoswiss-mdr/precipattractor | pyscripts/read_plot_statistics.py | Python | gpl-3.0 | 30,288 | [
"NetCDF"
] | 8af5e67777be1d1bf5fb3b22994e12ddc8d40e5701249f6a2e13d6ddac32a779 |
# BEGIN_COPYRIGHT
#
# Copyright (C) 2014 CRS4.
#
# This file is part of hadoop-galaxy, released under the terms of the BSD
# 3-Clause License <http://opensource.org/licenses/BSD-3-Clause>.
#
# END_COPYRIGHT
from glob import glob
import imp
import logging
import os
import sys
import unittest
_log = logging.getLogger(... | crs4/hadoop-galaxy | utils/unit_test_runner.py | Python | bsd-3-clause | 1,831 | [
"Galaxy"
] | 5eac1862220dc689c93ac61ba825a6a5f72383baaa68d377b1f8a9d4fe72efdc |
# -*- coding: utf-8 -*-
{
'(Recipient)': '(Empfänger)',
"'Cancel' will indicate an asset log entry did not occur": "'Abbrechen' zeigt an, dass ein Asset Log Eintrag nicht eingetreten ist",
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group loc... | nck0405/ChennaiEden | languages/de.py | Python | mit | 287,136 | [
"VisIt"
] | 1439ebb507da1883fa85c30b3c8ab2f16973c631ffa58920e49f515139a67ca7 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | nudles/incubator-singa | test/python/test_onnx.py | Python | apache-2.0 | 64,684 | [
"Gaussian"
] | 7b3a2bfb10397071844334266179f68e450b1ad20e71c08228e9c5b6490115f5 |
# -*- coding: utf-8 -*-
"""
sphinx.writers.texinfo
~~~~~~~~~~~~~~~~~~~~~~
Custom docutils writer for Texinfo.
:copyright: Copyright 2007-2011 by the Sphinx team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
import re
import string
import textwrap
from os import path
from docutils imp... | superdesk/Live-Blog | documentor/libraries/Sphinx-1.1.3-py3.2/sphinx/writers/texinfo.py | Python | agpl-3.0 | 44,657 | [
"VisIt"
] | efb71ed98281630fbd1f0cd2fd6b55d8b9ea0cfee2cea077944b491c20ada06d |
#!/usr/bin/python
import pysam
import string
import argparse
# The MIT License (MIT)
# Copyright (c) [2014] [Peter Hickey (peter.hickey@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 S... | PeteHaitch/Lister2BAM | Python/Lister_style_3_to_bam.py | Python | mit | 13,328 | [
"pysam"
] | 1a45ab66aa8bbb94a7c8380a5a1bb8f52ad33fbcbd37abaaf112089b3d206f84 |
"""
Copyright (C) 2004-2015 Pivotal Software, Inc. All rights reserved.
This program and the accompanying materials are made available under
the terms of the 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
... | rvs/gpdb | src/test/tinc/tinctest/models/concurrency/__init__.py | Python | apache-2.0 | 15,427 | [
"VisIt"
] | 411578372c88625bb14318e6c7ec65dbfee9d9b90b2667b19139390f077d050c |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2006 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | beernarrd/gramps | gramps/plugins/tool/rebuild.py | Python | gpl-2.0 | 3,587 | [
"Brian"
] | 37c8089e82af6548b524d52ec106293d9fa45bb69d98f6d30eea7b81bbd82297 |
'''
Created on Mar 17, 2012
@author: hampt
'''
import os
import commands
from Logger import Logger
from BlastWrapper import blastallParameters, createBlastPGPCommand
from metastudentPkg.commons import p, splitBigFastaFile
import sys
import shlex
import subprocess
import time
def runBlast(inputFilePath, blastDatabas... | Rostlab/MetaStudent | metastudentPkg/runMethods.py | Python | gpl-2.0 | 7,135 | [
"BLAST"
] | 0e3c2dce5e1bc11bb2e43082cbcfbc2f62377e8a67f4d04c819cbbcc5be34e31 |
"""Joint variant calling with multiple samples: aka squaring off, or backfilling.
Handles the N+1 problem of variant calling by combining and recalling samples
previously calling individually (or in smaller batches). Recalls at all positions found
variable in any of the input samples within each batch. Takes a general... | brainstorm/bcbio-nextgen | bcbio/variation/joint.py | Python | mit | 8,435 | [
"pysam"
] | 3d0894d4666a096308bdfbf858b42a348d3d53faf55cafa5a1491b0759fbfccf |
# Copyright (C) 2010-2019 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 v... | KaiSzuttor/espresso | testsuite/python/observable_profileLB.py | Python | gpl-3.0 | 7,716 | [
"ESPResSo"
] | 8f17a625e50d54dbd5decda93fe5063c86fd6eb2d386dfacc2883cbc862c5d41 |
r"""OS routines for NT or Posix depending on what system we're on.
This exports:
- all functions from posix, nt or ce, e.g. unlink, stat, etc.
- os.path is either posixpath or ntpath
- os.name is either 'posix', 'nt' or 'ce'.
- os.curdir is a string representing the current directory ('.' or ':')
- os.pardir... | dyyi/moneybook | venv/Lib/os.py | Python | apache-2.0 | 35,422 | [
"VisIt"
] | 5df03288f86a413e8c9c7290bffdc944b3b9a521473c564f95fe0749965a7723 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import numpy as np
from fractions import Fraction
try:
from math import gcd
except ImportError:
from fractions import gcd
from itertools import groupby... | czhengsci/pymatgen | pymatgen/transformations/advanced_transformations.py | Python | mit | 47,794 | [
"pymatgen"
] | 76718b99b5e7ab9d595bf5ccf356a0d37007e67cec1607d0f855f69823492809 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/controls/editors/one2manyeditor.py | Python | gpl-2.0 | 9,012 | [
"VisIt"
] | 43f3744dd9d936f0f14cc4c4b9ad5421369ad737d7ae287ab445afa1ce2d1b1a |
# IPython log file
# cd ~/projects/play
# make sure cache.py is around
get_ipython().run_line_magic('run', '-i cache.py')
_correlate_sparse_offsets.inspect_types()
_correlate_sparse_offsets.inspect_types(pretty=True)
get_ipython().run_line_magic('run', '-i cache.py')
get_ipython().run_line_magic('pinfo', '_correlate_... | jni/useful-histories | numba-experiments.py | Python | bsd-3-clause | 5,075 | [
"Gaussian"
] | cce029aa5e991b39dad332d18ad1536e128c5d6150bf82a431166ad50aace066 |
# Author: Ilan Schnell <ischnell@enthought.com>
# Copyright (c) 2008, Enthought, Inc.
# License: BSD Style.
# TODO: should derive from HasTraits
import csv
# FIXME: see loadtxt.py (should really be the loadtxt from numpy)
from mayavi.tools.data_wizards.loadtxt import loadtxt
class Sniff(object):
""" Sniff a CS... | liulion/mayavi | mayavi/tools/data_wizards/csv_sniff.py | Python | bsd-3-clause | 6,242 | [
"Mayavi"
] | bd60ca450f99e6c98a883b33af478d36e8f9930f114085866cf1a0e9a1951ac9 |
# -*- coding: utf-8 -*-
#@author: ilyass.tabiai@polymtl.ca
#@author: rolland.delorme@polymtl.ca
#@author: patrickdiehl@lsu.edu
import pkgutil
vtk_loader = pkgutil.find_loader('vtk')
found_vtk = vtk_loader is not None
if found_vtk == True:
import vtk
## Handles the output of the simulation results to vtk unstrucutr... | lm2-poly/PeriPyDIC | peripydic/IO/vis.py | Python | gpl-3.0 | 15,318 | [
"VTK"
] | 75bdfcab07c720c727d379b218a49a53708056fc5be3968e591b69d12ae66463 |
# -*- coding: utf-8 -*-
"""Module modeling a Multilayer Perceptron, featuring a tiny example
Example
-------
Executing this script will run a test consisting on training two linearly
separable set of points
$ python mlp.py
On the other hand, we can import this module and instanciating an ... | zentonllo/gcom | pr3/mlp.py | Python | mit | 23,483 | [
"NEURON"
] | 93564df92683400ca227e90ca307b0fcb3240dcaab64b3d3938f59b1ca3ea204 |
from Firefly.helpers.automation.automation import Automation | Firefly-Automation/Firefly | Firefly/helpers/automation/__init__.py | Python | apache-2.0 | 60 | [
"Firefly"
] | b86a03eaadbbbf9658aa4501a561971a68179ad37f6d4d61f8140f71570e62ce |
#!/usr/bin/env python
import argparse
import euston.io as io
import euston.helper as helper
parser = argparse.ArgumentParser(description='Performance analysis of CP2K output files.')
parser.add_argument('input', type=str, help='CP2K log file')
def main(parser):
args = parser.parse_args()
cp2k = io.Cp2kLog(args.i... | ferchault/euston | src/tools/es_cp2kperf.py | Python | lgpl-3.0 | 1,047 | [
"CP2K"
] | 481d9ed11d3c053d372718a20f79bcdfebffcea0dfd3ca4d5946b7a6177e625f |
# -*- coding: utf-8 -*-
"""
==========================================================
Create a new coordinate class (for the Sagittarius stream)
==========================================================
This document describes in detail how to subclass and define a custom spherical
coordinate frame, as discussed in ... | MSeifert04/astropy | examples/coordinates/plot_sgr-coordinate-frame.py | Python | bsd-3-clause | 10,549 | [
"Galaxy"
] | c88d69822c26010cca4285308b165b3d5efdab79c8d300ef36f315f194552d65 |
# (C) British Crown Copyright 2010 - 2014, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | Jozhogg/iris | lib/iris/tests/test_io_init.py | Python | lgpl-3.0 | 5,523 | [
"NetCDF"
] | 463c87297f66f3e2f2c5e62af5cae85d130aeb666ffa8bd994037cf8bdcb496a |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | ychfan/tensorflow | tensorflow/python/ops/gradients_impl.py | Python | apache-2.0 | 40,251 | [
"VisIt"
] | 357944735e0cc5d189f43e31f5ee2f090c680274a563d1140436731a45679897 |
#!/usr/bin/env python
# Copyright 2015 The Kubernetes 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 appli... | vfreex/kubernetes | cluster/juju/layers/kubernetes-worker/reactive/kubernetes_worker.py | Python | apache-2.0 | 46,014 | [
"CDK"
] | 7ea40b6a9a5b07b16571e15445b7bf817fad9560f1853b588586d65cba052a73 |
"""
Acceptance tests for the teams feature.
"""
from ..helpers import UniqueCourseTest
from ...pages.lms.teams import TeamsPage
from nose.plugins.attrib import attr
from ...fixtures.course import CourseFixture
from ...pages.lms.tab_nav import TabNavPage
from ...pages.lms.auto_auth import AutoAuthPage
from ...pages.lms.... | shubhdev/openedx | common/test/acceptance/tests/lms/test_teams.py | Python | agpl-3.0 | 4,564 | [
"VisIt"
] | e7a014e23777dea6f74a55c7af21982c5ecf8cbbd8940d8502ef3f86426132ec |
# Expectation Maximization Lecture
%matplotlib inline
import itertools
import numpy as np
import matplotlib.pyplot as plt
import matplotlib as mpl
import scipy
import scipy.spatial
from scipy import linalg
from sklearn.cluster import KMeans
from sklearn import mixture
np.random.seed( 2507365 ) # We'll set the rando... | kephale/TuftsCOMP135_Spring2016 | Lecture16/notebooks/Lecture16.py | Python | apache-2.0 | 7,354 | [
"Gaussian"
] | 16d19d6f8d3fc9cdc036c6d56890e1cb239a97ffba44a12a98f6d6032186c967 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import glob
import os
import subprocess
from io import open
import sys
from setuptools import setup, find_packages, Extension
try:
from numpy.distutils.misc_util import get_numpy_include_dirs
except Impor... | sonium0/pymatgen | setup.py | Python | mit | 4,715 | [
"ABINIT",
"ASE",
"FEFF",
"Gaussian",
"NWChem",
"VASP",
"VTK",
"pymatgen"
] | ca6eaa8379eb51cac770636c9ac2497aa8aca27f5faa025c1ed9fcf14e3068c8 |
# ===============================================================================
# Copyright 2021 ross
#
# 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/LICE... | USGSDenverPychron/pychron | pychron/core/stats/idw.py | Python | apache-2.0 | 6,555 | [
"Gaussian"
] | 209dd1593c93894ca2361025dbade01162b0cd6400d9fc233e3b6e8bc127e09b |
# $Id$
#
# Copyright (C)2003-2010 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.
#
""" Hybrid EState-VSA de... | strets123/rdkit | rdkit/Chem/EState/EState_VSA.py | Python | bsd-3-clause | 3,368 | [
"MOE",
"RDKit"
] | 4423c18fbb0705153f51b1e1ae0166a683a39c50c69861a54145c60fb07a7e1b |
import sys
import warnings
import _nemo as _n
_n.init()
def deprecated(func):
"""This is a decorator which can be used to mark functions
as deprecated. It will result in a warning being emitted
when the function is used."""
def new_func(*args, **kwargs):
warnings.warn("Call to deprecated func... | brainstudio-team/NeMo | src/api/python/wrappers.py | Python | gpl-2.0 | 14,847 | [
"NEURON"
] | 117c52e14ea040f208309871dce23ef624241f67f2ce5cc1632f4ce560603a86 |
#!/usr/bin/env python
#coding: utf-8
#### CLASSES ####
class fasta():
"""
"""
def __init__(self):
"""
"""
self.fastaDict = {}
#### FUNCTIONS ####
def fasta_reader(self, fastaFile):
"""
"""
fastaDict = {}
subHeader("Fasta reader")
... | brguez/TEIBA | src/python/clusterClippedReads.py | Python | gpl-3.0 | 25,308 | [
"pysam"
] | 41c2de8e7ea0c4cf51e59a6d8f8e68907d257bafe1b785c557c240de6b3cced8 |
import numpy as np
import pytest
import scipy.stats as stats
@pytest.fixture(scope='function')
def dimensions():
return 3
@pytest.fixture(scope='function')
def observations():
return 25
@pytest.fixture(scope='function')
def iterations():
return 1000
@pytest.fixture(scope='function')
def data(dimensi... | IamGianluca/algorithms | ml/tests/conftest.py | Python | mit | 730 | [
"Gaussian"
] | 2b79d300678c5f8e2df868db771b68386af7e2cc9866765bb259b874dd1a414f |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | alxgu/ansible | lib/ansible/modules/network/avi/avi_sslkeyandcertificate.py | Python | gpl-3.0 | 5,906 | [
"VisIt"
] | 1cd6c5fdb1e04ec04c7cbce7afa992678be7d2dcfddfed56a1ff4b12f3e80cca |
"""Test scriptlet to add an additional ball into play"""
# add_a_ball.py
# Mission Pinball Framework
# Written by Brian Madden & Gabe Knuth
# Released under the MIT License. (See license info at the end of this file.)
from mpf.system.scriptlet import Scriptlet
class AddABall(Scriptlet):
def on_load(self):
... | jabdoa2/mpf | machine_files/demo_man/scriptlets/add_a_ball.py | Python | mit | 1,631 | [
"Brian"
] | 5f7166465aedf40201ee8f1447b9b148cd0bdea2d476f1de32f735bc3f9cd93b |
import pandas as pd
from sklearn.ensemble import RandomForestClassifier
from sklearn.ensemble import GradientBoostingClassifier
from sklearn.ensemble import BaggingClassifier
from sklearn.ensemble import AdaBoostClassifier
from sklearn.ensemble import ExtraTreesClassifier
from sklearn.neural_network import MLPClassifie... | rupakc/Kaggle-Compendium | Stay Alert - The Ford Challenge/ford_baseline.py | Python | mit | 3,772 | [
"Gaussian"
] | 12692cec6c5304a23c73238092cdec7fb690b20092ae7c0ef46f57b42c57e300 |
#!/usr/bin/env python
"""
Install.py tool to download, unpack, build, and link to the LATTE library
used to automate the steps described in the README file in this dir
"""
from __future__ import print_function
import sys, os, subprocess, shutil, tarfile
from argparse import ArgumentParser
sys.path.append('..')
from ... | stanmoore1/lammps | lib/latte/Install.py | Python | gpl-2.0 | 4,571 | [
"LAMMPS"
] | 47175d2c572ee378d86ab26cbc2fa14299e89dbdd450f6fa76e8c4557898b8ac |
##################################################################
##
## MoPLUGS main menu
##
## Author Sergey Solohin (Neill3d) 2014-2016
## e-mail to: s@neill3d.com
## www.neill3d.com
##
## Github repo - https://github.com/Neill3d/MoPlugs
## Licensed under BSD 3-clause
## https://github.com/Neill3d/MoPlug... | Neill3d/MoPlugs | PythonScripts/Startup/MoPlugs_menu.py | Python | bsd-3-clause | 12,583 | [
"VisIt"
] | 0416f97b1d830e26d0875b73ced691fcd6f4bda5858f58f8a37110867b21ea96 |
#!/usr/bin/env python
"""
Show how the posterior gets updated as a set of coin tosses are generated for a biased coin.
Assume a flat prior on the bias weighting and also a Gaussian prior.
"""
import matplotlib.pyplot as pl
from scipy.stats import norm, kstest
import numpy as np
# set plot to render labels using late... | mattpitkin/GraWIToNStatisticsLectures | figures/scripts/coin_toss_2.py | Python | mit | 1,891 | [
"Gaussian"
] | 2aa54a9e0bbc5223d4de4c62615c654d9ccdddd496c9521244620b0c3e5827f6 |
# $HeadURL: $
''' FTSstorageUnbanAction
'''
from DIRAC import gConfig, gLogger, S_ERROR, S_OK
from DIRAC.Interfaces.API.DiracAdmin import DiracAdmin
from DIRAC.ResourceStatusSystem.PolicySystem.Actions.BaseAction import BaseAction
from D... | marcelovilaca/DIRAC | ResourceStatusSystem/PolicySystem/Actions/FTSStorageUnbanAction.py | Python | gpl-3.0 | 2,800 | [
"DIRAC"
] | 8489683cbd53a54e8aa52ee020a96a52565d36847d5c3f047265d24397970021 |
"""
Extended math utilities.
"""
# Authors: Gael Varoquaux
# Alexandre Gramfort
# Alexandre T. Passos
# Olivier Grisel
# Lars Buitinck
# License: BSD 3 clause
import warnings
import numpy as np
from scipy import linalg
from scipy.sparse import issparse
from . import check_random_st... | johnowhitaker/bobibabber | sklearn/utils/extmath.py | Python | mit | 18,306 | [
"Gaussian"
] | 07221364e2ba90a9d49d6488d521d23aa4c91612d9dad67128a39654577f2ac9 |
#! /usr/bin/env python3
#
# SCANIT - Control A spectrometer and collect data
#
# LICENSE:
# This work is licensed under the Creative Commons Zero License
# Creative Commons CC0.
# To view a copy of this license, visit
# http://directory.fsf.org/wiki/License:CC0
# or send a letter to:
# Creative Commons, PO Box 1866, M... | jluscher/SCANIT | scanit_v033.py | Python | cc0-1.0 | 86,949 | [
"VisIt"
] | 0f3f39f0ab69fcc13b883f8436de21ecd61507074ed6a8491b178a32348d2057 |
#!/usr/bin/env python
import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib.collections import LineCollection
from matplotlib.colors import colorConverter
import numpy as np
import re
import sys
import argparse
import os.path
def get_fermi(fname):
with open(fname) as myfile:
for line in... | mailhexu/pyDFTutils | pyDFTutils/plot/wannier_band_plot.py | Python | lgpl-3.0 | 8,300 | [
"Wannier90"
] | bcadd1783b4fc980977ed49f60b4ce141c948f53a1b6226e4c4c0154f894e7ad |
from .test_utils import TempDirectoryTestCase
from lwr.managers.base import JobDirectory
from lwr.tools.validator import ExpressionValidator
from os.path import join
class ValidatorTest(TempDirectoryTestCase):
def test_literal(self):
xml = """
<command_validator>
<literal value="top... | jmchilton/lwr | test/validator_test.py | Python | apache-2.0 | 9,029 | [
"Bowtie"
] | 484fc11d89a535a787ee1e57c64a853a356dc8de55479daf63188447201e5b5d |
"""
Some generic utility routines for number handling and
calculating (specific) variances
"""
import logging
import itertools
import numpy
from tkp.utility import containers
from tkp.utility.memoize import Memoize
from tkp.sourcefinder import utils
from tkp.sourcefinder import stats
from tkp.sourcefinder import extra... | transientskp/tkp | tkp/sourcefinder/image.py | Python | bsd-2-clause | 39,254 | [
"Gaussian"
] | 0c1e60717278a27ada6b884715a14f7950d20c0d9b2d660993c2d37573822eab |
import logging, threading, time
from Queue import Queue, Empty
from galaxy import config, util, model, tools, jobs
log = logging.getLogger( __name__ )
# This class is designed to provide job dispatch fairness for Galaxy users. It uses a
# dictionary of session (key) Queue (value) pairs to ensure no user (se... | volpino/Yeps-EURAC | lib/galaxy/jobs/schedulingpolicy/roundrobin.py | Python | mit | 6,801 | [
"Galaxy"
] | 5eecbecac2ca149a3a794bf4f765ddd210384f2a022cf17a5d816298c3c004fd |
from intermol.forces.abstract_type import AbstractType
class AbstractAngleType(AbstractType):
__slots__ = ['bondingtype1', 'bondingtype2', 'bondingtype3', 'c']
def __init__(self, bondingtype1, bondingtype2, bondingtype3, c=False):
"""An abstract representation of a generic angle type. """
sup... | shirtsgroup/InterMol | intermol/forces/abstract_angle_type.py | Python | mit | 551 | [
"Desmond"
] | c4b5f215274caba6e91a27fd9d49b020b6e32cc427264d385f18f26e4078850f |
########################################################################
# File : InProcessComputingElement.py
# Author : Stuart Paterson
########################################################################
""" The simplest Computing Element instance that submits jobs locally.
This is also the standard "CE" ... | fstagni/DIRAC | Resources/Computing/InProcessComputingElement.py | Python | gpl-3.0 | 4,670 | [
"DIRAC"
] | 7ccded491ae0a520d591f195dd7494451be902f7cf61e1a81bfe7003aae4cf1a |
from __future__ import print_function
from bose_einstein import bose_einstein
from constant import htr_to_K, htr_to_meV, htr_to_THz
import argparser
import numpy as np
args = argparser.read_argument('Renormalize EPW calculation')
window = args.energy / htr_to_meV
if args.vb: offset = -8.75333295715961e-03
else: offset... | mmdg-oxford/papers | Schlipf-PRL-2018/model/epw_lifetime.py | Python | gpl-3.0 | 1,370 | [
"EPW"
] | 86c735b6e7751ff028c652f808999d6f6d3cb1cd9c4e1c2b118562f5b3480cd6 |
# -*- coding: utf-8 -*-
# Cypress -- A C++ interface to PyNN
# Copyright (C) 2016 Andreas Stöckel
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or... | hbp-sanncs/cypress | resource/backend/pynn/binnf.py | Python | gpl-3.0 | 14,039 | [
"NEURON"
] | 3ab253f7da351e9c92d38a3a218c5bebbe609f6f44bccecbe921f0c0e860fc86 |
from __future__ import print_function, division
import unittest, numpy as np
from pyscf import gto, scf
from pyscf.nao import gw as gw_c
class KnowValues(unittest.TestCase):
def test_si_ref(self):
""" This is GW """
mol = gto.M( verbose = 1, atom = '''H 0 0 0; H 0.17 0.7 0.587''', basis = 'cc-pvdz',)
g... | gkc1000/pyscf | pyscf/nao/test/test_0053_gw_si_ref.py | Python | apache-2.0 | 522 | [
"PySCF"
] | 2fbe7f512f24dfe478bac2c07a09c7907f7d75603c892eb01acbca93bde3d444 |
# -*- coding: utf-8 -*-
'''
*******************************************************************
* File: validation.py
* Description:
* Author: HarshaRani
* E-mail: hrani@ncbs.res.in
********************************************************************/
/********************************... | BhallaLab/moose-core | python/moose/SBML/validation.py | Python | gpl-3.0 | 4,606 | [
"MOOSE"
] | a562181f2d9e2888f6308f53a971e92da2f0135276f5fc225e49e62f6835ea47 |
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