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# -*- coding: utf8 -*-
#
# Copyright 2011 Kyrre Ness Sjøbæk
# This file is part of AcdOpti.
#
# AcdOpti 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 you... | kyrsjo/AcdOpti | src/acdOpti/AcdOptiMeshInstance.py | Python | gpl-3.0 | 16,922 | [
"NetCDF"
] | 605ea331c2f8377b7b33e2bb2726c7367deafe3251b815111e3adfa6c6624996 |
# Copyright (C) 2015 Atsushi Togo
# All rights reserved.
#
# This file is part of phono3py.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must retain the above copyright
# noti... | atztogo/phono3py | phono3py/cui/create_supercells.py | Python | bsd-3-clause | 5,706 | [
"VASP",
"phonopy"
] | 7c359f70c4b836f28a97fedcab2b6394e5d6816d930185af70162cd5914848b7 |
# The Archives team:
# <Adam Guy> adam@adam-guy.com AKA "Adam01"
# <Andrew Godwin> andrew@aeracode.org AKA "Aera"
# <Dylan Lukes> lukes.dylan@gmail.com AKA "revenant"
# <Gareth Coles> colesgareth2@hotmail.com AKA "gdude2002"
#
# And,
#
# T... | TheArchives/Nexus | core/plugins/isoimage.py | Python | bsd-2-clause | 4,195 | [
"VisIt"
] | 17a08a5e460333e0b7e775bf8e0f7ee6fcf2c485a27989c0b5b42a6a42785bee |
""" Module that holds the DataStore Client class
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import time
import random
import copy
import threading
from DIRAC import S_OK, S_ERROR, gLogger, gConfig
from DIRAC.Core.Base.Client imp... | ic-hep/DIRAC | src/DIRAC/AccountingSystem/Client/DataStoreClient.py | Python | gpl-3.0 | 6,271 | [
"DIRAC"
] | c7dc33e6393ca7295a4d8c5ec25cea9cdd763734d485d917897db629f04150a9 |
from ase import Atom, Atoms
from gpaw.test import equal
from gpaw import GPAW, mpi
from gpaw.lrtddft import LrTDDFT
import numpy
#numpy.seterr(all='raise')
txt='-'
txt='/dev/null'
load = False
#load = True
if not load:
R=0.7 # approx. experimental bond length
a = 3
c = 4
H2 = Atoms([Atom('H', (a... | qsnake/gpaw | gpaw/test/apmb.py | Python | gpl-3.0 | 2,319 | [
"ASE",
"GPAW"
] | 4db5d872cff805c90cca2e1f66878ad9585ce8ddeeba9d428251cc4ee734f4b2 |
#!/mnt/lustre_fs/users/mjmcc/apps/python2.7/bin/python
##!/Library/Frameworks/Python.framework/Versions/2.7/bin/python
# ----------------------------------------
# USAGE:
# ----------------------------------------
# PREAMBLE:
import numpy as np
from numpy.linalg import *
import MDAnalysis
from MDAnalysis.analysis.ali... | rbdavid/Water_Dynamics | Water_diffusion/water_diffusion.py | Python | gpl-3.0 | 13,594 | [
"MDAnalysis",
"VMD"
] | 7f3e72426efd2e9d9b1dd45c38f243e535738488ff6994993e4f8e0b67a509c2 |
'''
Check a pile of blast output files and a list of genomes and report which genomes were not found
I also print out the results of those we need
'''
import os,sys
import re
try:
blastdir=sys.argv[1]
wantedf=sys.argv[2]
outputdir=sys.argv[3]
except:
sys.exit(sys.argv[0] + " <blast output directory> <... | linsalrob/PhageHosts | code/extract_phage_mg_blast.py | Python | mit | 1,521 | [
"BLAST"
] | 924a49f7bcd7c0a3d778ed97307dcd1680ead0785bbf843a7daf92e282c1226e |
import unittest
import time
import multiprocessing
from pychemia.db import has_connection
from pychemia import pcm_log
from pychemia.searcher import HarmonySearch, FireFly, GeneticAlgorithm, ParticleSwarm
from pychemia.population import LJCluster
def evaluator():
from pychemia.evaluator import cluster_launcher
... | MaterialsDiscovery/PyChemia | tests/test_searcher_clusters.py | Python | mit | 2,998 | [
"Firefly"
] | a55cfaf72cb18e8ad3666b080119dffb33c0e5ac885aed20e51bfad93975ca1b |
#!/usr/bin/env python
__author__ = 'greg'
import pymongo
import random
import os
import time
from time import mktime
from datetime import datetime,timedelta
import numpy as np
from scipy.stats import ks_2samp
import cPickle as pickle
from scipy.stats import beta
import matplotlib.pyplot as plt
from scipy.special import... | camallen/aggregation | experimental/paper/confidence/blankConfidence.py | Python | apache-2.0 | 8,294 | [
"Brian"
] | 1cd15936014ca3d0281e7dd30dbefad89f7e5a3dd57b94bb341a41420e1bec08 |
# -*- coding: utf-8 -*-
#!/usr/bin/python
"""Test of sayAll output of Firefox on the Orca wiki.
"""
from macaroon.playback import *
import utils
sequence = MacroSequence()
########################################################################
# We wait for the focus to be on a blank Firefox window.
#
sequence.app... | h4ck3rm1k3/orca-sonar | test/keystrokes/firefox/sayAll_wiki.py | Python | lgpl-2.1 | 9,811 | [
"ORCA"
] | d9ae65160bf3953ae2a461e6d9624cb92e79095ca48d3c95c76769cb0418f0e7 |
# -*- coding: UTF-8 -*-
"""
``bowtie2_mapper`` :sup:`*`
-----------------------------------------------------------------
:Authors: Menachem Sklarz
:Affiliation: Bioinformatics core facility
:Organization: National Institute of Biotechnology in the Negev, Ben Gurion University.
A module for running bowtie2 mapper:
... | bioinfo-core-BGU/neatseq-flow_modules | neatseq_flow_modules/main_NSF_classes/mapping/bowtie2_mapper.py | Python | gpl-3.0 | 10,008 | [
"Bowtie"
] | 5c570f8f43a1c2a9dcba3e10991c4b2b73d4277f04a712d3aff3e63621295923 |
#!/usr/bin/env python
# This script produces graphs in a similar format to Fig 2.4 on page 46 of
# http://www.springer.com/cda/content/document/cda_downloaddocument/9783642218149-c1.pdf
import numpy as np
from matplotlib import pyplot
from scipy import constants
import csv
cdata = []
with open('../xray_attenuation... | darkstar007/xseeker | data/atmosphere/atmospheric_fraction.py | Python | gpl-3.0 | 3,150 | [
"Avogadro"
] | afb7724486d883129acb04f5f9a1c8f1c5cd5e15cf29245049eedf3138d676df |
from sim.api import *
from sim.basics import *
import Queue
import random
"""
Link State Router.
Global state with LSpacket transmission.
Local computation with Breadth First Search.
"""
class LSRouter (Entity):
def __init__(self):
"""
self.routingTable(dict): key: router, value: through which port... | zhaoyan1117/RoutingProtocols | ls_router.py | Python | bsd-3-clause | 6,857 | [
"VisIt"
] | c837b4eeb10960d53d7d7cee94b7e3e988708db1247890de573e182e45520909 |
from __future__ import absolute_import
import base64
import re
import os
import sys
import urllib
PY3 = sys.version_info[0] == 3
if PY3:
from io import StringIO
from io import BytesIO
basestring = str
else:
from StringIO import StringIO
try:
import json
except ImportError:
import simplejson ... | dimka665/dropbox | dropbox/client.py | Python | mit | 67,654 | [
"VisIt"
] | 1f2a577f768fe3af4c8fc38c47a0d1f5ff3b4c45717a19a9177bec1eb5c52f25 |
# 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... | laosiaudi/tensorflow | tensorflow/python/ops/control_flow_grad.py | Python | apache-2.0 | 8,756 | [
"VisIt"
] | 28e74eaa57dc0f3ebc1ec52310e0f403b981ee008cf44e83ab943dfda55bfeee |
from math import floor
from world import World
import Queue
import SocketServer
import datetime
import random
import re
import requests
import sqlite3
import sys
import threading
import time
import traceback
DEFAULT_HOST = '0.0.0.0'
DEFAULT_PORT = 4080
DB_PATH = 'craft.db'
LOG_PATH = 'log.txt'
CHUNK_SIZE = 32
BUFFER... | TakSyak/Craft | bin/server.py | Python | mit | 24,728 | [
"VisIt"
] | bd26495a2bce2fac30a36437976e1290f7c51365ca16212ae96f5e1ddb3c13de |
#!/usr/bin/env python
###############################################################################
##
## Copyright (C) 2014-2015, New York University.
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is par... | hjanime/VisTrails | scripts/system_info.py | Python | bsd-3-clause | 3,286 | [
"VTK"
] | 2f012fc11da90492d659d70599c7b7d3e8d88994e0d4ef4813f279f1f59d4fde |
"""
Analysis of Voronoi diagrams based on scipy.spatial.
class Voronoi: Compute and analyse Voronoi diagrams.
"""
import numpy as np
import scipy.spatial as sp
class Voronoi:
"""
Input points
------------
The points from the Voronoi diagram is constructed.
ndim: int
The dimension o... | jfsehuanes/thunderfish | thunderfish/voronoi.py | Python | gpl-3.0 | 44,337 | [
"Gaussian"
] | 778e82ce0c8f8f7dc174c884cb24f714cef79f3dcfe1824ebe1eb0f90d429034 |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | RomainBrault/scikit-learn | sklearn/tree/tree.py | Python | bsd-3-clause | 49,309 | [
"Brian"
] | cfac4280dc2fb0d96ecb1e98d5c8117e5771d19a00e2229092ef0dea31696fbd |
import mdp
try:
from pyNN.pcsim import *
from pypcsim import *
except ImportError:
pass
try:
import brian
except ImportError:
pass
import scipy
from Oger.utils import spikes_to_states, inputs_to_spikes
class BrianIFReservoirNode(mdp.Node):
def __init__(self, input_dim, output_dim, dtype, input... | npinto/Oger | Oger/nodes/spiking_nodes.py | Python | gpl-3.0 | 15,176 | [
"Brian"
] | 14e7495424e4dcae46dcd45b645cf5dece1d11e7ebd07dd351ef9b8d9cc29193 |
#!/usr/bin/env python2
import urllib2 # for fetching weather data
import json # for parsing weather data
import re # for parsing the format string
import argparse # for parsing CLI args
import os.path # for getting the path to the profiles
# Current version information
PROGRAM_NAME = '... | velentr/winfo | winfo.py | Python | mit | 6,658 | [
"Brian"
] | fa11aef31f9ef3009ff909419fa1c9cd9600db9411d8399752eb7765d0491cb5 |
from numpy import zeros,empty
from pylab import plot,show
# Constants
N = 26
C = 1.0
m = 1.0
k = 6.0
omega = 2.0
alpha = 2*k-m*omega*omega
# Set up the initial values of the arrays
A = zeros([N,N],float)
for i in range(N-1):
A[i,i] = alpha
A[i,i+1] = -k
A[i+1,i] = -k
A[0,0] = alpha - k
A[N-1,N-1] = alpha ... | KiMiralles/Python-Learning | Computational Physics Newman/Book Resources/springs.py | Python | gpl-3.0 | 873 | [
"Gaussian"
] | c276dfe1215d683eac09bc17e8c5eed9c35ac19f197b0580e8a6337531c583cc |
import logging
import wx
from service.fit import Fit
from gui.bitmap_loader import BitmapLoader
import gui.globalEvents as GE
from gui.preferenceView import PreferenceView
from service.settings import EOSSettings
import gui.mainFrame
logger = logging.getLogger(__name__)
class PFFittingEnginePref(PreferenceView):
... | bsmr-eve/Pyfa | gui/builtinPreferenceViews/pyfaEnginePreferences.py | Python | gpl-3.0 | 5,969 | [
"CRYSTAL"
] | 6adc5a7f5e14de11beafed11a519a3f6eec4af24b0c3c7cd48e5df9e47178b93 |
import os
import sys
import time
start = time.time()
triangle_file = sys.argv[1] if len(sys.argv) == 2 else "big_triangle.txt"
print "node using '%s'" % triangle_file
file_path = os.path.abspath(os.path.join(os.path.dirname(__file__),
triangle_file))
# method to integerify ... | bertrandvidal/stuff | triangle/node_triangle.py | Python | unlicense | 2,192 | [
"VisIt"
] | 57c982817e9536542a3c18c18a30ed3e1ab3f6a8df2017768e778854a565203e |
#This dataset was pulled off Kaggle.com as under the dataset named "Predict'em All at the link below
#https://www.kaggle.com/semioniy/predictemall
#The data describes pokemon sightings in the mobile game Pokemon Go, developed by Niantic. In the game, players use a mobile
# device's GPS capability to locate, captur... | MichaelMKKang/Projects | Kaggle_Projects/PokemonGO predictions.py | Python | mit | 16,417 | [
"Gaussian"
] | f4e62091fb3539279386b7dcb5e6b78e50c193dfe051883cebba8a51a26f129d |
"""Functionality to query and extract information from aligned BAM files.
"""
import collections
import contextlib
import os
import itertools
import subprocess
import numpy
import pysam
import toolz as tz
from bcbio import utils
from bcbio.bam import ref
from bcbio.distributed import objectstore
from bcbio.distribute... | hjanime/bcbio-nextgen | bcbio/bam/__init__.py | Python | mit | 16,701 | [
"pysam"
] | 82e49308ab915c48b48cc54b2a2bf7d197cd4ff9e5bc1832239eeced6e251e68 |
# Displays important features of the snappyHexMeshDict
# To be run using "Tools -> Python Shell -> Run Script" inside of paraFoam
# assumes that one OpenFOAM-case is opened
from PyFoam.RunDictionary.ParsedParameterFile import ParsedParameterFile
from PyFoam.Paraview import caseDirectory
from PyFoam.Paraview.SimpleS... | mortbauer/openfoam-extend-Breeder-other-scripting-PyFoam | examples/paraview3/snappyDisplay.py | Python | gpl-2.0 | 1,407 | [
"ParaView"
] | a32f88bc29da61fb04bab0e36fd661b067e62657a6e3e0deaf652b6b2a7892a3 |
#!/bin/python3
# coding: utf-8
"""
A Sphinx extension that enables RST includes from remote sources.
https://github.com/kallimachos/chios
Copyright (C) 2021 Brian Moss
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 So... | kallimachos/chios | chios/remoteinclude/__init__.py | Python | gpl-3.0 | 2,411 | [
"Brian"
] | 81263b240f58d53190174c1d5f1142ba4266e34afaa5d06b2678330d64d09d8c |
"""
FEniCS program for the deflection w(x,y) of a membrane:
-Laplace(w) = p = Gaussian function, in a unit circle,
with w = 0 on the boundary.
"""
from dolfin import *
import numpy
if not has_cgal():
import sys
sys.exit(0)
# Set pressure function:
T = 10.0 # tension
A = 1.0 # pressure amplitude
R = 0.3 ... | maciekswat/dolfin_1.3.0 | test/unit/book/python/chapter_1_files/stationary/poisson/membrane1.py | Python | gpl-3.0 | 2,144 | [
"Gaussian"
] | d34e853ccaf921262878a79537fa8f88c1eb60d8119f4c0413716bb6481fd9a6 |
#!/usr/bin/env python
from argparse import ArgumentParser
parser = ArgumentParser(description="""Use Mayavi to plot a static spherical
harmonic with a chosen angular degree and azimuthal order. """)
parser.add_argument('-l', '--ell', type=int, default=6,
help="angular degree (default=6)")
parser... | warrickball/figures | sph_harm_mlab.py | Python | gpl-3.0 | 4,592 | [
"Mayavi"
] | b733a9bc1987f197b474cbf9303addea9fb3b532f40ac6e2ad113bd821e136a3 |
#!/usr/bin/env python
from numpy import loadtxt, zeros
try:
from netCDF4 import Dataset as NC
except:
from netCDF3 import Dataset as NC
from getopt import getopt, GetoptError
from sys import exit, argv
from time import asctime
GRIP_FILE = 'sum89-92-ss09-50yr.stp'
SPEC_FILE = 'specmap.017'
DT_FILE = 'grip_dT.n... | JohannesFeldmann/pism | examples/old/eisgreen/eiscore.py | Python | gpl-2.0 | 4,243 | [
"NetCDF"
] | 0aaa9d9b7176bacaf878a5e4df721a00b068a6a1254f78923fb5fd1a3ed6ccef |
# coding: utf-8
# In[ ]:
"""Summary of tensorflow basics.
Parag K. Mital, Jan 2016."""
# In[13]:
# %% Import tensorflow and pyplot
import numpy as np
import tensorflow as tf
import matplotlib.pyplot as plt
# In[ ]:
# %% tf.Graph represents a collection of tf.Operations
# You can create operations by writing o... | ds-hwang/deeplearning_udacity | python_practice/01_basics.py | Python | mit | 4,919 | [
"Gaussian"
] | 35d31189bc637deb02fa8bc4d66c2c9457025bacc1c7299a6e61635900056d2d |
import logging
import sys
import time
import numpy as np
import emcee
from espei.error_functions import calculate_zpf_error, calculate_activity_error, \
calculate_non_equilibrium_thermochemical_probability, \
calculate_equilibrium_thermochemical_probability
from espei.priors import PriorSpec, build_prior_specs
... | PhasesResearchLab/ESPEI | espei/optimizers/opt_mcmc.py | Python | mit | 14,984 | [
"Gaussian"
] | 90fa1fa689a5b77b865c5bd944688355d233a3b40b35c40e99fee0453d6c6d5b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2013 Radim Rehurek <me@radimrehurek.com>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""
Deep learning via word2vec's "skip-gram and CBOW models", using either
hierarchical softmax or negative sampling [1]_ [2]_.
The train... | xuxiandi/gensim | gensim/models/word2vec.py | Python | gpl-3.0 | 72,092 | [
"VisIt"
] | c11f2c57d70e4d00b5a4ba571ce1749e3d7dd5d4acb1bcf713bfa4e6ede870e0 |
# Copyright (C) 2019-2020
# Max Planck Institute for Polymer Research & JGU Mainz
#
# 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 ... | espressopp/espressopp | src/vectorization/__init__.py | Python | gpl-3.0 | 1,002 | [
"ESPResSo"
] | 7e9b38010f3cd4cbd53ad202f06913c9cbe7d9d0292b89851bd4d86e87840fa9 |
# Copyright (C) 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 versio... | espressomd/espresso | testsuite/scripts/samples/test_lj_liquid_structurefactor.py | Python | gpl-3.0 | 1,027 | [
"ESPResSo"
] | 68546d6c921cfcde74ca809c707e52d88cae9c970c7eed3b670d79b180a7f0c5 |
#!/usr/bin/env python
"""
Script to reset metadata on all Tool Shed repositories installed into a Galaxy instance. The received
API key must be associated with a Galaxy admin user.
usage: reset_metadata_on_installed_repositories.py key
Here is a working example of how to use this script.
python ./reset_metadata_on_i... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/scripts/api/reset_metadata_on_installed_repositories.py | Python | gpl-3.0 | 1,139 | [
"Galaxy"
] | a3005650fa933e6504677d98955f4e292e89386f21caebaa9c29a0376685f399 |
"""
A collection of functions to find the weights and abscissas for
Gaussian Quadrature.
These calculations are done by finding the eigenvalues of a
tridiagonal matrix whose entries are dependent on the coefficients
in the recursion formula for the orthogonal polynomials with the
corresponding weighting function over ... | kmspriyatham/symath | scipy/scipy/special/orthogonal.py | Python | apache-2.0 | 23,623 | [
"Gaussian"
] | 9971fbb0a16f4679c2e258154ed6f1004b3ab57524f6768d00260bf38d731977 |
#! /usr/bin/python
# -*- coding: utf-8 -*-
"""
Module is used for visualization of segmentation stored in pkl file.
"""
import os.path
import os.path as op
import sys
path_to_script = os.path.dirname(os.path.abspath(__file__))
sys.path.append(os.path.join(path_to_script, "../extern/dicom2fem/src"))
from loguru import... | mjirik/imtools | imtools/show_segmentation.py | Python | mit | 18,835 | [
"ParaView",
"VTK"
] | 2f164d95887c74cbd9667ffe9fa4ff1c9b4fc8fadef97c7a12252a515594afa8 |
#!/usr/bin/env python
# *-* coding: UTF-8 *-*
# Copyright 2012-2020 Ronald Römer
#
# 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 ... | zippy84/vtkbool | examples/python/csg_model_making/band.py | Python | apache-2.0 | 12,303 | [
"VTK"
] | 42a0da059b6ac61e13cd59b55c079399db61ca2343c86f7843d884850782d68e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
import math
import re
import os
import textwrap
import warnings
from collections import OrderedDict, deque
import six
from six.moves import zi... | nisse3000/pymatgen | pymatgen/io/cif.py | Python | mit | 55,573 | [
"Avogadro",
"CRYSTAL",
"pymatgen"
] | e539cf25e76e1b6e267209081f062c1a13f351f1e9aa94bcfcf853ac56cc2db4 |
"""
Processes for Species distribution
Author: Nils Hempelmann (nils.hempelmann@lsce.ipsl.fr)
"""
from pywps.Process import WPSProcess
from flyingpigeon.sdm import _SDMINDICES_
from flyingpigeon.log import init_process_logger
import logging
logger = logging.getLogger(__name__)
class sdmcsvProcess(WPSProcess):
... | KatiRG/flyingpigeon | flyingpigeon/processes/wps_sdm_csv.py | Python | apache-2.0 | 14,840 | [
"NetCDF"
] | 7f3c0b0f1321646aa6b43ef3793065a8d6fafd45a3ca9d479b4d2af4f28b2ed3 |
paraview_plugin_version = '2.1.0'
from vtk.numpy_interface import dataset_adapter as dsa
# This is module to import. It provides VTKPythonAlgorithmBase, the base class
# for all python-based vtkAlgorithm subclasses in VTK and decorators used to
# 'register' the algorithm with ParaView along with information about UI.... | banesullivan/ParaViewGeophysics | PVPlugins/PVGeo_Filters.py | Python | bsd-3-clause | 33,159 | [
"ParaView",
"VTK"
] | 37edb741230dc2c78b0cdb1f8fa19e2545a9934159af069a3204efdbb6ba3462 |
##
## Java Information Dynamics Toolkit (JIDT)
## Copyright (C) 2012, Joseph T. Lizier
##
## This program is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation, either version 3 of the License, or
## (at yo... | jmmccracken/ECA | infodynamics-dist-1.2.1/demos/python/example6DynamicCallingMutualInfo.py | Python | mit | 5,582 | [
"Gaussian"
] | 9af4796035a1648cff1058b6cdc635b75ac4a096531e6e7608ba4641da3ce921 |
# Copyright (C) 2012 Swift Navigation Inc.
#
# This source is subject to the license found in the file 'LICENSE' which must
# be be distributed together with this source. All other rights reserved.
#
# THIS CODE AND INFORMATION IS PROVIDED "AS IS" WITHOUT WARRANTY OF ANY KIND,
# EITHER EXPRESSED OR IMPLIED, INCLUDING B... | cbeighley/peregrine | peregrine/acquisition.py | Python | gpl-3.0 | 23,262 | [
"Gaussian"
] | da607d4bff11ea1cabfeaa4faa9318d47df7e5f9c8ef8cf12d19de71f6e6850a |
#!/usr/bin/python
#E-Bv0.1
#This code for education purpose only.
#Use it at your own risk !!!
import os
import smtplib
import getpass
import sys
print '\n******************************************************'
print '\n* THIS IS ONLY FOR EDUCATIONAL PURPOSE *'
print '\n* AUTHOR: SWETABH... | Swetabhsuman8/SpamEm | SpamEm.py | Python | mit | 1,886 | [
"VisIt"
] | e1e7ec36d21d8ec543106c3bf17f4d18242804dfbe9303491ddb4445c078c55a |
from __future__ import absolute_import
import inspect
__all__ = ["Visitor"]
class Visitor(object):
"""
A generic visitor for a COFFEE AST.
To define handlers, subclasses should define :data:`visit_Foo`
methods for each class :data:`Foo` they want to handle.
If a specific method for a class :da... | gmarkall/COFFEE | coffee/visitor.py | Python | bsd-3-clause | 4,351 | [
"VisIt"
] | b1b587eb245928d5719aa6f44279145c0548e571419d71b6546a4ef426739fc0 |
#!/usr/bin/env python
'''
setup board.h for chibios
'''
import argparse, sys, fnmatch, os, dma_resolver, shlex, pickle, re
import shutil
parser = argparse.ArgumentParser("chibios_pins.py")
parser.add_argument(
'-D', '--outdir', type=str, default=None, help='Output directory')
parser.add_argument(
'--bootloade... | EShamaev/ardupilot | libraries/AP_HAL_ChibiOS/hwdef/scripts/chibios_hwdef.py | Python | gpl-3.0 | 52,154 | [
"CRYSTAL"
] | c11596609f7eade9e0bb4450e93f558466f9b7d295a726c706fceb2182e5d797 |
# -*- coding: utf-8 -*-
import os, sys
COMMON_DIR = os.path.abspath(os.path.dirname(os.path.dirname(__file__)))
PROJECT_DIR = os.path.dirname(COMMON_DIR)
ZIP_PACKAGES_DIRS = (os.path.join(PROJECT_DIR, 'zip-packages'),
os.path.join(COMMON_DIR, 'zip-packages'))
# Overrides for os.environ
env_ext = {... | wooyek/nuntio | web/common/appenginepatch/aecmd.py | Python | mit | 4,874 | [
"VisIt"
] | 9a856c3af5ee5b3a263dee7a4a991e13f5699be909e0dd6b886a83d09ff918a4 |
from ase.lattice import bulk
from gpaw import GPAW, FermiDirac
def groundstate(a, k):
si = bulk('Si', 'diamond', a)
si.calc = GPAW(kpts=(k, k, k),
xc='PBE',
gpts=(20, 20, 20),
occupations=FermiDirac(0.01),
parallel={'domain': 1, 'band':... | robwarm/gpaw-symm | doc/tutorials/pbe0/si_pbe.py | Python | gpl-3.0 | 423 | [
"ASE",
"GPAW"
] | 3306ea0ac1db129d8a5b92a5f11e4a0c68831c10bf56fe4fb6c64fca01276a0e |
__author__ = "Andre Merzky, Ole Weidner"
__copyright__ = "Copyright 2012-2013, The SAGA Project"
__license__ = "MIT"
""" SAGA job interface """
import radical.utils.signatures as rus
from saga.constants import SYNC, ASYNC, TASK
from saga.job.constants import *
import saga.adaptors.base as sa... | PanDAWMS/pilot | saga/job/job.py | Python | apache-2.0 | 24,229 | [
"Galaxy"
] | a751993e918222ac4b5c8495ab2a28f433e39a9ddac510eab20a0c107aa95c0b |
##########################################################################################
## _______ .______ ______ .__ __. _______ ______ _______ _______ ##
## | \ | _ \ / __ \ | \ | | | ____| / || ____|| \ ##
## | .--. || |_) | | | | | | \| | ... | dronecfd/droneCFD | droneCFD/Meshing.py | Python | gpl-2.0 | 9,669 | [
"ParaView"
] | 97d0baa5a7eb1f56bb01fa5f07246070cfba654fe4feab3ab72f91391e9646d0 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Kyle A. Beauchamp
# Contributors: Robert McGibbon, Matthew Har... | daviddesancho/mdtraj | mdtraj/tests/test_topology.py | Python | lgpl-2.1 | 7,462 | [
"MDTraj",
"OpenMM"
] | 35d6e3fca90bde44d2629e5c6a928c25dc093f7ee8446a5681c2c8a42130c12e |
# DNSChef is a highly configurable DNS Proxy for Penetration Testers
# and Malware Analysts. Please visit http://thesprawl.org/projects/dnschef/
# for the latest version and documentation. Please forward all issues and
# concerns to iphelix [at] thesprawl.org.
# Copyright (C) 2015 Peter Kacherginsky, Marcello Salvati... | CiuffysHub/MITMf | core/servers/DNS.py | Python | gpl-3.0 | 21,837 | [
"VisIt"
] | 889c2aeab0a48e8aec92c6db9147ea77007fb48f5ab595aac8e32915296c5c4a |
#!/usr/bin/env python
# Script for measuring response time for redmine urls.
# It attempts to authenticate via html form which is it given on first GET.
# It should work generally for anything that forwards properly, and has
# "username" and "password" fields in the form.
#
# I tested it for CASino login and standard ... | forgeservicelab/forge.benchmark | cas_log_in_and_measure.py | Python | mit | 4,515 | [
"CASINO"
] | adca4fdb65007a00a376a88845aa9ac1b55d52b510a83188d3e3eea005fbbae8 |
#
# Python External Attribute Library
#
# Copyright (C) 2016 Wayne Mogg All rights reserved.
#
# This file may be used under the terms of the MIT License
# (https://github.com/waynegm/OpendTect-External-Attributes/blob/master/LICENSE)
#
# Author: Wayne Mogg
# Date: March, 2016
# Homepage: http://waynegm.github.io/O... | waynegm/OpendTect-External-Attributes | Python_3/extlib.py | Python | mit | 30,118 | [
"Gaussian"
] | d67ea70115c08e4489f1ac79dfdedc8de2dc140967aea8575c348e235ad40e3e |
#!/usr/bin/env python
#
# Copyright 2007 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law o... | CollabQ/CollabQ | .google_appengine/google/appengine/tools/appcfg.py | Python | apache-2.0 | 88,766 | [
"VisIt"
] | bf15bfe4bf20a227d524530ff7b88619048ebb996dd7252b98d3f873677c14ed |
# Functions to create and write SOCRATES NetCDF files for use with Cl_run_cdf.
from netCDF4 import *
import os
# Writes some quantity x as a function of pressure p_lev
def write_latlon(path, x, prefix, suffix, name, unit, title,
p_lev=None, basis=None):
if p_lev is not None and basis is not None:
print('Er... | DavidSAmundsen/socrates_tools | cmn/read_write_socrates_netcdf.py | Python | mit | 2,229 | [
"NetCDF"
] | 4e1b974c5f5aba4224d3dc762c85d6cb33d13f5bac75f6239abfd8810f738cfb |
# 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 http://mozilla.org/MPL/2.0/.
import os
from os.path import curdir
import errno
#-------------------------------------------------------------------... | luser/socorro | socorro/external/fs/filesystem.py | Python | mpl-2.0 | 6,552 | [
"VisIt"
] | ac26e0192ae6d961cd3aef962b57d6ef82786e25e4b76502cfdfd54e5916d9b1 |
# -*- coding: utf-8 -*-
"""Functions for building node predicates."""
from typing import Any, Callable, Iterable, List, Union
from .node_predicates import concatenate_node_predicates, invert_node_predicate
from .typing import NodePredicate
from ..graph import BELGraph
from ...constants import CONCEPT, NAME
from ...d... | pybel/pybel | src/pybel/struct/filters/node_predicate_builders.py | Python | mit | 6,494 | [
"Pybel"
] | 3bbd19ea389c9838dd651656024e44e69893cc1c603c33f63ec10ee003064ff3 |
# -*- coding: utf-8 -*-
# transformations.py
# Copyright (c) 2006-2012, Christoph Gohlke
# Copyright (c) 2006-2012, The Regents of the University of California
# Produced at the Laboratory for Fluorescence Dynamics
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modifica... | chrisjsewell/ipymd | ipymd/shared/transformations.py | Python | gpl-3.0 | 72,269 | [
"CRYSTAL"
] | 2d996cc181b51edf3c59954dd63a7689cddf759ca5fd04174ee559d3cd3b8693 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/test/test_0158_bse_h2o_uhf_cis.py | Python | apache-2.0 | 2,108 | [
"PySCF"
] | 2053ebb0146a656b9dddfdb08d0417c5a46df791d71426da5b21d6eb9cb04dc1 |
from pycparser import c_generator, c_ast
class AbstractCGenerator(c_generator.CGenerator):
def visit_Constant(self, n):
return "CONST"
def visit_ID(self, n):
return "ID"
def visit_ArrayRef(self, n):
arrref = "ARR"
return arrref + '[' + self.visit(n.subscript) + ']'
d... | saeedanabtawi/CodeVisionCommandline | Loader/helper.py | Python | mit | 3,007 | [
"VisIt"
] | 21d2253e41e14b5aa1719909d126e86e981bd3ac4277d75562c3571f5053cd5f |
#! /usr/bin/env python3
# -*- 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 requi... | googleapis/python-os-config | scripts/fixup_osconfig_v1alpha_keywords.py | Python | apache-2.0 | 6,933 | [
"VisIt"
] | 22fd60a3eb6c6161281992628417cf432b2f3948dd69edb63c663087ae4cb282 |
#!/usr/bin/env python
__author__ = "waroquiers"
import json
import os
import unittest
from pymatgen.analysis.chemenv.coordination_environments.chemenv_strategies import (
AngleNbSetWeight,
CNBiasNbSetWeight,
DeltaCSMNbSetWeight,
DeltaDistanceNbSetWeight,
DistanceAngleAreaNbSetWeight,
Distanc... | materialsproject/pymatgen | pymatgen/analysis/chemenv/coordination_environments/tests/test_weights.py | Python | mit | 33,121 | [
"pymatgen"
] | b7a7bdb5c6ed9160f4c958e2d9eda89b04f64a6a0e926503d4531a11db730ffc |
"""
Tests for transformer objects.
"""
from __future__ import division
from __future__ import unicode_literals
from deepchem.molnet import load_delaney
from deepchem.trans.transformers import FeaturizationTransformer
__author__ = "Bharath Ramsundar"
__copyright__ = "Copyright 2016, Stanford University"
__license__ = ... | Agent007/deepchem | deepchem/trans/tests/test_transformers.py | Python | mit | 21,771 | [
"Gaussian"
] | 94b85b49402811a9b3841050129ab5c1da0e57aed7de2330a4c5681cdabd2538 |
from __future__ import unicode_literals
import logging
from django.db.models import Manager
from djblets.db.managers import ConcurrencyManager
from reviewboard.accounts.trophies import trophies_registry
class ProfileManager(Manager):
"""Manager for user profiles."""
def get_or_create(self, user, *args, **... | chipx86/reviewboard | reviewboard/accounts/managers.py | Python | mit | 5,041 | [
"VisIt"
] | 1569acb01d88b543186f5de3580de1f8fb96e016cfaf79b99d04002a4f162626 |
# -*- coding: utf-8 -*-
u"""SRW template fixups
:copyright: Copyright (c) 2019 RadiaSoft LLC. All Rights Reserved.
:license: http://www.apache.org/licenses/LICENSE-2.0.html
"""
from __future__ import absolute_import, division, print_function
from pykern import pkcollections
from pykern.pkdebug import pkdc, pkdexc, pk... | mrakitin/sirepo | sirepo/template/srw_fixup.py | Python | apache-2.0 | 2,619 | [
"CRYSTAL"
] | d32c69d42e9daf90de1274a335e90312feb4fb774d6efca825c1e5675554daeb |
#* 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/lgpl-2.1.html
import loggi... | harterj/moose | python/MooseDocs/extensions/heading.py | Python | lgpl-2.1 | 1,480 | [
"MOOSE"
] | 2e3b41b5a7add1739c498d337cdfd1650d2154f10b4db333d0343674205e146f |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 16.3.8
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | 0x46616c6b/ansible | lib/ansible/modules/network/avi/avi_applicationprofile.py | Python | gpl-3.0 | 6,694 | [
"VisIt"
] | 739c101c7ac484e77b97e373b4e4f2bd0be269a2700a1fa1be48b0f29c5c45f6 |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
# XXX
# XXX
# XXX Use random number generator objects
# XXX
# XXX
"""Main gpaw module.
Use like this::
from gpaw import Calculator
"""
import os
import sys
try:
from distutils.util import get_platform
except Imp... | qsnake/gpaw | gpaw/__init__.py | Python | gpl-3.0 | 9,297 | [
"GPAW"
] | 09a6743da4194a69a0ee0560d1dddd83e9804e1b4297ade9249aa469ac2ce0d0 |
##############################################################################
# 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... | tmerrick1/spack | var/spack/repos/builtin/packages/gdl/package.py | Python | lgpl-2.1 | 4,412 | [
"NetCDF"
] | b73251154e82a2717076bb99eadc3a543532d89c2de11cba982fb6919813e301 |
# -*- coding: utf-8 -*-
"""
Created on Fri Jan 02 09:38:14 2015
@author: Anna Stuhlmacher
plotting
"""
from __future__ import division, absolute_import
import logging
import numpy as np
import scipy as sp
import scipy.interpolate as spinterp
import time
import datetime as dt
import matplotlib.pyplot as plt
from matp... | jswoboda/GeoDataPython | GeoData/plotting.py | Python | mit | 38,354 | [
"Mayavi"
] | aab402eea116f0f8a3912e19b3cd4e0079b57b8a2b067ed64d9b196114ef5aed |
"""
Tests browser instantiation, selection, etc
"""
import os
import shutil
import socket
import tempfile
from unittest import TestCase
from unittest.mock import patch
import pytest
from selenium import webdriver
from selenium.common.exceptions import WebDriverException
import bok_choy.browser
from bok_choy.promise ... | edx/bok-choy | tests/test_browser.py | Python | apache-2.0 | 14,527 | [
"VisIt"
] | bc98954f162c0629d5ab4c0c39d151454e650cd419121bab43272ac03f16d022 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
This file is part of XBMC Mega Pack Addon.
Copyright (C) 2014 Wolverine (xbmcmegapack@gmail.com)
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 Softwar... | xbmcmegapack/plugin.video.megapack.dev | resources/data/keywords.py | Python | gpl-3.0 | 16,869 | [
"VisIt"
] | 7f9c39dfc9934a490f0e353615bd18a48c82650785431957fdf8cc047aa97123 |
"""
============================================================
Empirical evaluation of the impact of k-means initialization
============================================================
Evaluate the ability of k-means initializations strategies to make
the algorithm convergence robust as measured by the relative stan... | loli/sklearn-ensembletrees | examples/cluster/plot_kmeans_stability_low_dim_dense.py | Python | bsd-3-clause | 4,334 | [
"Gaussian"
] | f6386568191a316caef63027560bcd7cb08f3f6d4fe05df745d31d43052b2b3c |
#!/usr/bin/env python3
import sys
from pathlib import Path
import psutil
import os
import warnings
from pathlib import Path
if not sys.getfilesystemencoding():
sys.getfilesystemencoding = lambda: 'UTF-8'
import numpy as np
import datetime
from collections import OrderedDict
from little_helpers import fix_requests_... | JannickWeisshaupt/OpenDFT | src/main.py | Python | gpl-3.0 | 169,561 | [
"ABINIT",
"CRYSTAL",
"Quantum ESPRESSO",
"VTK",
"exciting"
] | 8c76b3e53cfaec188ce544d16840b047dcd07044310d33b396d4d18a4dbac4ca |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class REdger(RPackage):
"""Empirical Analysis of Digital Gene Expression Data in R
Diffe... | LLNL/spack | var/spack/repos/builtin/packages/r-edger/package.py | Python | lgpl-2.1 | 1,811 | [
"Bioconductor"
] | ff6f3ca6ff1f6cfe18154b3a8232d1003e20e0757414cf7ca629ac8cd1c451c1 |
import math
import numpy as np
from scipy.optimize import minimize
from scipy.special import logsumexp
from .utils import softmax
def _safe_exp(x):
x = min(x, 500)
return math.exp(x)
class PairwiseFcts:
"""Optimization-related methods for pairwise-comparison data.
This class provides methods... | lucasmaystre/choix | choix/opt.py | Python | mit | 8,242 | [
"Gaussian"
] | d2c400230d27cef85b73ed81a236ebf0dfe2ffb60439c736b93da7af06dedf23 |
# -*- coding: utf-8 -*-
#
# Copyright © 2018 Mark Wolf
#
# This file is part of scimap.
#
# Scimap 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 lat... | m3wolf/scimap | tests/test_pawley_refinement.py | Python | gpl-3.0 | 6,933 | [
"Gaussian"
] | b66795da25c3433553700a8cb45f11ad83e46c5e45b8c531507b522d21cd07ec |
"""
pyqremis
"""
from functools import partial
from inspect import getmro
__author__ = "Brian Balsamo"
__email__ = "brian@brianbalsamo.com"
__version__ = "0.0.3"
def lowerFirst(s):
if not s:
return s
return s[0].lower() + s[1:]
def iter_wrap(thing, callback):
if isinstance(thing, list) or \
... | bnbalsamo/pyqremis | pyqremis/__init__.py | Python | gpl-3.0 | 43,069 | [
"Brian"
] | 024a727e14203f73a3e0dacc06af873dac2a5b7436aea1be5d8b9681522307d7 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
from django.views import defaults as default_views
urlpat... | rjpen516/openevmap | server/openevmaps/config/urls.py | Python | gpl-3.0 | 1,740 | [
"VisIt"
] | 2c1348887824bdee1578fd3427e354f138ef197f5dc2924f9b7adfcedc7b83b4 |
# -*- coding: utf-8 -*-
from setuptools import setup
setup (
name='vaspirin',
packages=['vaspirin'],
version='2.0',
description='Painless VASP post-processing tool',
author='Daniel S. Koda, Ivan Guilhon',
author_email='danielskoda@gmail.com, ivanguilhonn@gmail.com ',
url='http://www.gmsn.ita.br/',
d... | dskoda/vasp-ita | setup.py | Python | gpl-3.0 | 782 | [
"VASP"
] | 4ef136bbcccf4b93022a41ac30ae36541e4bfc538c7ffd2ba911392a0d78782c |
""" Collection of user jobs for testing purposes
"""
# pylint: disable=wrong-import-position, invalid-name
from __future__ import print_function
import unittest
import time
from DIRAC.tests.Utilities.testJobDefinitions import helloWorld, mpJob, parametricJob
from DIRAC import gLogger
gLogger.setLevel('DEBUG')
from ... | petricm/DIRAC | tests/System/unitTestUserJobs.py | Python | gpl-3.0 | 3,207 | [
"DIRAC"
] | 98c8b405c1277baca569f5d8dc0c49f26bb8d4846e67246cb323b69b774f0730 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
import json
import warnings
from pymatgen import SETTINGS
from pymatgen.core.structure import Structure
from pymatgen.transformations.standard_transformations import \
Substituti... | gVallverdu/pymatgen | pymatgen/alchemy/tests/test_materials.py | Python | mit | 6,066 | [
"VASP",
"pymatgen"
] | 4f8761179f00d296afc12dc287ae28d970ea601d6c852f704ee1d9069e42d9ab |
import os
def validate_existing_path(field: str, value: str, error):
if not os.path.isabs(value):
error(field, f"path <{value}> is not an absolute path!")
if not os.path.exists(value):
error(field, f"path <{value}> does not exist!")
def validate_path(field: str, value: str, error):
if no... | KrasnitzLab/sgains | sgains/configuration/schema.py | Python | mit | 9,512 | [
"BWA",
"Bowtie"
] | 932de95ed863efdfb99369bc5c683fc4f13adbff237cbfc61154c83535d2b51c |
#
# Copyright (C) 2013,2014,2015,2016 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)... | KonradBreitsprecher/espresso | samples/lj_liquid.py | Python | gpl-3.0 | 6,290 | [
"ESPResSo"
] | 02cdfa5761a4052675df2d93c66744faa96949e046df79a0a7fd6e633f4a0faa |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2016, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License... | halberom/ansible | lib/ansible/modules/system/systemd.py | Python | gpl-3.0 | 16,931 | [
"Brian"
] | 27e8f31b39513076a1e2c06b833153f723df68f51d0b183b40631ca2379d4a91 |
import logging
import re
from pandas import DataFrame
from pandas import read_csv
from pandas.io.common import EmptyDataError
from os import path
from . import recurse_in_dir_and_apply_fn
from . import utils
from . import i2b2_connection
################################################################################... | LREN-CHUV/i2b2-import | i2b2_import/features_csv_import.py | Python | apache-2.0 | 7,976 | [
"VisIt"
] | 510ef48f0dd2fe85ac33ef491abb687dda3d8000e223603b3355f6809b25a124 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General... | le9i0nx/ansible | lib/ansible/modules/network/avi/avi_prioritylabels.py | Python | gpl-3.0 | 4,276 | [
"VisIt"
] | a0c50d0bad134f11c6f4c696d3f2651ef8edb0328645c09b027f591b4c5ec3de |
# coding: utf-8
# Copyright (c) Materials Virtual Lab.
# Distributed under the terms of the BSD License.
from __future__ import division, unicode_literals, print_function
"""
#TODO: Replace with proper module doc.
"""
from pymatgen.ext.matproj import MPRester
import json
from monty.serialization import dumpfn
import... | matk86/pymatgen | pymatgen/cli/pmg_query.py | Python | mit | 1,919 | [
"pymatgen"
] | e91aedb6365a55ecb6aa4a0c7bb08b9c539bb1cc3b2bcf70f144f5cc5d03ad3d |
import os
import numpy as np
from netCDF4 import Dataset
from compliance_checker.acdd import ACDD1_1Check, ACDD1_3Check
from compliance_checker.tests import BaseTestCase, pytestBaseTest
from compliance_checker.tests.helpers import MockTimeSeries, MockVariable
from compliance_checker.tests.resources import STATIC_FIL... | ioos/compliance-checker | compliance_checker/tests/test_acdd.py | Python | apache-2.0 | 21,190 | [
"NetCDF"
] | bf4d8b7a4b46dc427db9b9a5726f8bfac2d446411bdd48d29d96462dfdfc06b2 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from BeautifulSoup import BeautifulSoup as bs
import urllib2
import urllib
import HTMLParser
import sys
import json
import re
try:
from addon.common.net import Net
except:
print 'Failed to import script.module.addon.common'
xbmcgui.Dialog().ok... | natko1412/repo.natko1412 | zips/plugin.video.pftvso/pftvso.py | Python | gpl-2.0 | 11,256 | [
"VisIt"
] | b6c4f1d8be304bd4da76fa3e9fb91d9408c134b5567d92b7551f9a7c94942794 |
""" DIRAC FileCatalog plug-in class to manage dynamic datasets defined by a metadata query
"""
__RCSID__ = "$Id$"
import hashlib
import os
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities.List import stringListToString
class DatasetManager( object ):
_tables = dict()
_tables["FC_MetaDatasets"... | arrabito/DIRAC | DataManagementSystem/DB/FileCatalogComponents/DatasetManager.py | Python | gpl-3.0 | 29,470 | [
"DIRAC"
] | 3fe06ecaeb2495e8570536bb8ce06a1211d36907af6a15184baa66d6142c7d6f |
############################ Copyrights and license ############################
# #
# Copyright 2012 Christopher Gilbert <christopher.john.gilbert@gmail.com> #
# Copyright 2012 Steve English <steve.english@navetas.com> ... | PyGithub/PyGithub | github/Repository.py | Python | lgpl-3.0 | 159,891 | [
"Brian"
] | 6a1824e38447181bc01675f58a19494f2a1256485cf7035fa67740cf02877b89 |
'''
(c) GeneGenie Bioinformatics Ltd. 2018
Licensed under the MIT License.
To view a copy of this license, visit <http://opensource.org/licenses/MIT/>.
@author: neilswainston
'''
# pylint: disable=invalid-name
# pylint: disable=wrong-import-order
from sklearn.metrics import classification_report, confusion_matrix
... | synbiochem/synbiochem-learn | gg_learn/study/thermostability.py | Python | mit | 1,206 | [
"VisIt"
] | a4df2f999009ab85b6824e3480ad84e98b37053bd970a822f86a97335218d657 |
# multicomp_lif.py ---
#
# Filename: multicomp_lif.py
# Description: Leaky Integrate and Fire using regular neuronal compartment
# Author: Subhasis Ray
# Maintainer:
# Created: Fri Feb 7 16:26:05 2014 (+0530)
# Version:
# Last-Updated:
# By:
# Update #: 0
# URL:
# Keywords:
# Compatibility:
#
#
# Commen... | BhallaLab/moose | moose-examples/snippets/multicomp_lif.py | Python | gpl-3.0 | 6,199 | [
"MOOSE",
"NEURON"
] | a89b03ed41d883b6449be8b17aabd7bc29634ed438e03078f7f9f1343ab473f7 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | kdmurray91/scikit-bio | skbio/metadata/_mixin.py | Python | bsd-3-clause | 13,199 | [
"scikit-bio"
] | 2962451cfae8132b65be55dee95bbcf930fd8f2e406c561ff2fedc5acab7d635 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under th... | alejob/mdanalysis | package/MDAnalysis/coordinates/XTC.py | Python | gpl-2.0 | 4,669 | [
"Gromacs",
"MDAnalysis"
] | bf6fe9d72c39f3d44bf2cd5a1dea9ce83100dac125556f7166541276736a336d |
#
# 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/learn/ray/tf/conftest.py | Python | apache-2.0 | 1,265 | [
"ORCA"
] | 96e7683ff22a889f745ec10f9e6bbdcee49fea20177f6d4f4ec4cf978d24d6b1 |
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