text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
"""
/******************************************************************************
This source file is part of the Avogadro project.
Copyright 2013 Kitware, Inc.
This source code is released under the New BSD License, (the "License").
Unless required by applicable law or agreed to in writing, software
di... | wadejong/avogadrolibs | avogadro/qtplugins/quantuminput/inputGenerators/gaussian.py | Python | bsd-3-clause | 5,874 | [
"Avogadro",
"Gaussian"
] | e45b384a7ab58081b40303f6d0659c100f61a4e74949c6888760dfd20eea7684 |
# Online haptic_map implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
import tf
import os
#import hrl_lib.mayavi2_util as mu
i... | tapomayukh/projects_in_python | rapid_categorization/haptic_map/outlier/online_map_outlier_no_model.py | Python | mit | 17,767 | [
"Gaussian",
"Mayavi"
] | 40cf38b4aaabb971550d9d02439c406356181306e19861bbf4bb1e23dab8c7fc |
# Orca
#
# Copyright 2009 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This libr... | chrys87/orca-beep | src/orca/generator.py | Python | lgpl-2.1 | 43,334 | [
"ORCA"
] | 848b82f34a014ffd31136f1416ef268fa81ac4dad8361debbb10bd88db8693db |
#!/usr/bin/python
########################################################################
# 9 Jan 2015
# Patrick Lombard, Centre for Stem Stem Research
# Core Bioinformatics Group
# University of Cambridge
# All right reserved.
########################################################################
import argparse
... | pdl30/pyngspipe | pyngspipe/tools.py | Python | gpl-2.0 | 6,001 | [
"Bowtie",
"HTSeq"
] | 1c7ad3c0569213482a4ca4107b51eb9bbd33866cf687e42f7b24423a812fbc3d |
import os
import unittest
import vtk, qt, ctk, slicer
from slicer.ScriptedLoadableModule import *
import logging
class SegmentEditorHollow(ScriptedLoadableModule):
"""Uses ScriptedLoadableModule base class, available at:
https://github.com/Slicer/Slicer/blob/master/Base/Python/slicer/ScriptedLoadableModule.py
""... | lassoan/SlicerSegmentEditorExtraEffects | SegmentEditorHollow/SegmentEditorHollow.py | Python | bsd-3-clause | 5,507 | [
"VTK"
] | 740d5397a8c63cc4997533e05a09b76691cae84f20120eb97efec8de4daa257a |
"""
Experiments on various real datasets. Vary the sample sizes.
"""
__author__ = 'wittawat'
import fsic.data as data
import fsic.feature as fea
import fsic.indtest as it
import fsic.glo as glo
import fsic.util as util
import fsic.kernel as kernel
import exglobal as exglo
# need independent_jobs package
# https:/... | wittawatj/fsic-test | fsic/ex/ex5_real_vary_n.py | Python | mit | 18,035 | [
"Gaussian"
] | a72a63e2452dd6d2ba8987937b43afb93ca330aeb705b7530b68a85ecf33a4b2 |
r"""
================================================================
Robust covariance estimation and Mahalanobis distances relevance
================================================================
An example to show covariance estimation with the Mahalanobis
distances on Gaussian distributed data.
For Gaussian dis... | RPGOne/Skynet | scikit-learn-c604ac39ad0e5b066d964df3e8f31ba7ebda1e0e/examples/covariance/plot_mahalanobis_distances.py | Python | bsd-3-clause | 6,232 | [
"Gaussian"
] | 08086619f4b3563b173d1381a12aca73363fd55935d500a20d9440205dc2f8b7 |
# Copyright 2014 The LUCI Authors. All rights reserved.
# Use of this source code is governed under the Apache License, Version 2.0
# that can be found in the LICENSE file.
"""Swarming bot code. Includes bootstrap and swarming_bot.zip.
It includes everything that is AppEngine specific. The non-GAE code is in
bot_arch... | luci/luci-py | appengine/swarming/server/bot_code.py | Python | apache-2.0 | 10,315 | [
"VisIt"
] | 780fe4d7c669b68082a7da75c14d3742273e45ada5f6fc8632714c3a0531eed5 |
from ase.dft import Wannier
from gpaw import restart
atoms, calc = restart('benzene.gpw', txt=None)
wan = Wannier(nwannier=18, calc=calc, fixedstates=15, file='wan18.pickle')
import pylab as pl
weight_n = pl.sum(abs(wan.V_knw[0])**2, 1)
N = len(weight_n)
F = wan.fixedstates_k[0]
pl.figure(1, figsize=(12, 4))
pl.bar(r... | grhawk/ASE | tools/doc/tutorials/wannier/plot_spectral_weight.py | Python | gpl-2.0 | 660 | [
"ASE",
"GPAW"
] | 265b57390d62887b6e3d41971a9be34bdda2fdc7b367aee158e29715007d1608 |
# f90wrap: F90 to Python interface generator with derived type support
#
# Copyright James Kermode 2011-2018
#
# This file is part of f90wrap
# For the latest version see github.com/jameskermode/f90wrap
#
# f90wrap is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser Gene... | jameskermode/f90wrap | f90wrap/parser.py | Python | lgpl-3.0 | 46,940 | [
"VisIt"
] | c0aafaa8344439ad448dec32773943e147b553961dafed4695bf05b0fde2412c |
# -*- coding: utf-8 -*-
"""
Functions to estimate specific differential phase (KDP) using various methods.
"""
from __future__ import division, print_function
import numpy as np
from numpy import linalg
from scipy.signal import firwin
from warnings import warn
from .calc_kdp_ray_fir import calc_kdp_ray_fir
# import ti... | tjlang/CSU_RadarTools | csu_radartools/csu_kdp.py | Python | gpl-2.0 | 10,729 | [
"Gaussian"
] | 553dc3db0196c7c54c643ea552c5d5420eacd1d6e148433f32bd8ef8aae26f4a |
#!/usr/bin/env python
'''!
@package rpgtoolbox.rpgtools
@file rpgtools.py
@brief RPG helpful functions
This module contains some helpful functions for role-playing games like:
- dice() for dic rolling
- getLvl() for calculate actual level of char
@date (C) 2015-2021
@license GNU V3.0
@author Marcus Schwamberger
@emai... | olmongol/rpg-tools | src/rpgtoolbox/rpgtools.py | Python | gpl-3.0 | 13,644 | [
"BWA"
] | 924774abfb1899b405575ef197a8dc46d7edfa99668c0ec8056c61e5c8a79a3f |
#! /usr/bin/env python3
# Script to clean out a file system such as scratch based on certain criteria
# (e.g. not accessed or modified in x days)
#
# archiving option
# /scratch/delete30/lastname_f/projectx/.archive-me is archived to
# /economy/lastname_f/archive/delete30/projectx-2014-08-21/
#
# fs-cleaner dirkpeters... | FredHutch/fs-cleaner | fs-cleaner.py | Python | apache-2.0 | 24,639 | [
"VisIt"
] | ab361765e6fc9f7d4f19d9d884313d98837e31a7eaf116a9abd14026f12638db |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <codecell>
import sys
sys.path.append('/home/will/PatientPicker/')
import pandas as pd
# <codecell>
import LoadingTools
store = pd.HDFStore('/home/will/HIVReportGen/Data/SplitRedcap/2013-01-16/EntireCohort.hdf')
pat_data = store['redcap']
# <codecell>
drug_col... | JudoWill/ResearchNotebooks | Untitled2.py | Python | mit | 5,582 | [
"VisIt"
] | 721af7b22edac582d6b85caacc7a3eed683c687b3a3521b37cebc2de96babd3e |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | vericred_client/models/state.py | Python | apache-2.0 | 17,064 | [
"VisIt"
] | cf5b6d20332a229bee10f90d58f6a2c5bc6423e486260df3fd139744d2ad628d |
import numpy, matplotlib
from CoolProp.HumidAirProp import HAProps
from CoolProp.Plots.Plots import InlineLabel
import numpy as np
import serial
from threading import Thread
import time
from datetime import tzinfo, timedelta, datetime
####################
# Setup for serial #
####################
last_r... | nfette/psychroplotter | PsychScript2.py | Python | gpl-2.0 | 6,222 | [
"exciting"
] | af747e8f346c684f5c5956d4b768ad9d2e153982f67e096d46cfa116c7a37542 |
# !usr/bin/env python
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2017-08-06 18:39:54
# @Last modified by: Brian Cherinka
# @Last Modified time: 2017-08-07 11:31:13
from __future__ import print_function, division, absolute_import
import warnings
class S... | havok2063/SciScript-Python | python/sciserver/exceptions.py | Python | apache-2.0 | 858 | [
"Brian"
] | 90700c997bdbbdc1e8d3943d76e21f3e1ac825810bfee5db4818bd2b712341af |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2013-2014 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms o... | pmghalvorsen/gramps_branch | gramps/plugins/textreport/familygroup.py | Python | gpl-2.0 | 33,501 | [
"Brian"
] | bba2debd7882655c963ea4a153768c142ce7f95841fde1bc2b8d48306e41f0d9 |
try:
import cProfile as myprofiler
except:
import profile as myprofiler
import orca.orca
myprofiler.run('orca.orca.main()', 'orcaprof')
| pvagner/orca | test/harness/runprofiler.py | Python | lgpl-2.1 | 144 | [
"ORCA"
] | df2e9b7770d776fc6cdd86ede4bced7a26d27787fd615e14e90d98e54733041e |
import telebot
from telebot.types import LabeledPrice, ShippingOption
token = '1234567890:AAAABBBBCCCCDDDDeeeeFFFFgggGHHHH'
provider_token = '1234567890:TEST:AAAABBBBCCCCDDDD' # @BotFather -> Bot Settings -> Payments
bot = telebot.TeleBot(token)
# More about Payments: https://core.telegram.org/bots/payments
prices ... | eternnoir/pyTelegramBotAPI | examples/payments_example.py | Python | gpl-2.0 | 4,286 | [
"VisIt"
] | 39748b63ee617b21b0ab3d82888021afeabbbc58fcb234f54de64fe30050112f |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | harterj/moose | python/TestHarness/testers/bench.py | Python | lgpl-2.1 | 14,760 | [
"MOOSE"
] | 6034a24db9b999549a5e90d877175488d978d52524a0da87289e227e292e28cd |
from flask import jsonify, Blueprint, request, json
from werkzeug.datastructures import MultiDict
from projectp import socketio
from projectp import db
from projectp.auth import requires_auth
from projectp.visits.forms import DateForm
from projectp.visits.models import Visit
from .models import Location
locations = ... | Proj-P/project-p-api | projectp/locations/views.py | Python | mit | 2,614 | [
"VisIt"
] | 573fc7d2530d2c86e572384ab1ca12d04c1d6439f873b3e589957b7587d2d486 |
#!python
# coding=utf-8
from __future__ import division
import os
import json
import math
import shutil
import argparse
import calendar
import tempfile
from glob import glob
from pathlib import Path
from datetime import datetime
from collections import OrderedDict
import pandas as pd
import netCDF4 as nc4
from compli... | SECOORA/GUTILS | gutils/nc.py | Python | mit | 24,414 | [
"NetCDF"
] | 2aa27aec19d65e876c5c1eb58f972b392fc7adf59af9218b9ef6f4461f06f6a1 |
#!/usr/bin/python
"""
Copyright 2012 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 of th... | druss316/G-Harvestor | html/getResourceTypeList.py | Python | gpl-3.0 | 2,692 | [
"Galaxy"
] | fb276a75328cb283ac5e21727c8276d2fe467dd362f1b34905dd5daf61335b45 |
"""Module to work with network in SIF format.
http://wiki.cytoscape.org/Cytoscape_User_Manual/Network_Formats#SIF_Format
"""
class SIFNode(object):
def __init__(self, id):
self.id = id
self.edges = []
self.reverse= []
class SIFEdge(object):
def __init__(self, type, target):
... | tryptochan/domain_utils | SIF.py | Python | mit | 5,228 | [
"Cytoscape"
] | 5841858ba4e46b040697b79c6e42b0dd3ff39d186b03dff574b0fc2a098eb86a |
"""
Step and impulse responses
==========================
These examples compare the analytical solution with `empymod` for time-domain
step and impulse responses for inline, x-directed source and receivers, for the
four different frequency-to-time methods **QWE**, **DLF**, **FFTLog**, and
**FFT**. Which method is fas... | prisae/empymod | examples/time_domain/step_and_impulse.py | Python | apache-2.0 | 13,182 | [
"DIRAC"
] | 2c5e3c688f9b2bbc724533119fc3fc4149190be54ae55b097805b608c2d09a7b |
import sys
sys.path.insert(1, "../../")
import h2o, tests
def offset_1388():
print "Loading datasets..."
pros_hex = h2o.import_file(tests.locate("smalldata/prostate/prostate.csv"))
pros_hex[1] = pros_hex[1].asfactor()
pros_hex[3] = pros_hex[3].asfactor()
pros_hex[4] = pros_hex[4].asfactor()
... | kyoren/https-github.com-h2oai-h2o-3 | h2o-py/tests/testdir_jira/pyunit_NOPASS_pubdev_1388_offset_comparisons.py | Python | apache-2.0 | 3,003 | [
"Gaussian"
] | 713c5bb54c00e8442cf524a32c4d4ff3a0f61a867f90a1e10f040859019152e1 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines filters for Transmuter object.
"""
import abc
from collections import defaultdict
from monty.json import MSONable
from pymatgen.analysis.structure_matcher import ElementComparator, StructureMatcher
f... | materialsproject/pymatgen | pymatgen/alchemy/filters.py | Python | mit | 12,546 | [
"pymatgen"
] | 6ba7e25d26e8fcf336d78e902760dc61dabaaee6e1d8dba194af2b91b0523168 |
""" This is a test of the creation of the pilot wrapper
"""
# pylint: disable=protected-access, invalid-name, no-self-use
import os
import base64
import bz2
from DIRAC.WorkloadManagementSystem.Utilities.PilotWrapper import pilotWrapperScript
def test_scriptEmpty():
""" test script creation
"""
res = pilotWra... | andresailer/DIRAC | WorkloadManagementSystem/Utilities/test/Test_PilotWrapper.py | Python | gpl-3.0 | 3,291 | [
"DIRAC"
] | fef8a2ae2cf2f0348af6ff41cb4b018c98e5b0cb82de1b917f3a2f731373036f |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/trilinos/package.py | Python | lgpl-2.1 | 32,336 | [
"NetCDF"
] | d0e3a3036e672ff76bcbaeea59535b9dafeaeb32348802c5d746b604e04aa0dc |
# Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
"""
Example: Thompson sampling for Bayesian Optimization with GPs
=============================================================
In this example we show how to implement Thompson sampling for Bayesian optimization with Gaussian process... | pyro-ppl/numpyro | examples/thompson_sampling.py | Python | apache-2.0 | 10,104 | [
"Gaussian"
] | 48990e3ad9c4be7f21e1b2e84fd9113c26dde43d6e7f632ea75fa435d3bbb67a |
#!/usr/bin/env python
"""
xds_profile_mitai.py
(c) RIKEN 2015. All rights reserved.
Author: Keitaro Yamashita
This software is released under the new BSD License; see LICENSE.
"""
import os, sys, math, re
def write_xplor_map(res, NX, NZ, filename):
ofs = open(filename, "w")
ofs.write("\n")
ofs.write("... | keitaroyam/yam_scripts | xds_profile_mitai.py | Python | bsd-3-clause | 4,154 | [
"PyMOL"
] | 6ec1b2f2a08109588f1323ce7f16ce63e32d645a2e6e1406dcc3aab3b18523e5 |
# This notebook has commands to download external data and software or parse
# external data. These shouldn't be stored on figshare because they are
# available over the web. In some instances I parse some of the external data
# into more useful formats.
import os
import shutil
import subprocess
import sys
from urllib... | frazer-lab/pipelines | cdpipelines/prepare.py | Python | mit | 42,543 | [
"Bioconductor",
"HTSeq"
] | d0467b5a7384932cac76d42da7f77b853a76de3e1929e2ffb5c71a87fdec75ac |
#!/usr/bin/python
#
# Copyright 2015 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by... | stitchfix/spinnaker | dev/refresh_source.py | Python | apache-2.0 | 24,119 | [
"ORCA"
] | 4bd5d42fdb3cdb5cfaeb0039aadf86068a9ec6a2aceeca6f8bf10a2eb4a6c3f2 |
'''
wrapper for lists of galaxy objects, each method returns lists, unless they
are setting attributes.
'''
import numpy as np
import itertools
from .starpop import StarPop
__all__ = ['Galaxies']
class Galaxies(StarPop):
'''
wrapper for lists of galaxy objects, each method returns lists, unless they
are... | philrosenfield/ResolvedStellarPops | galaxies/galaxies.py | Python | bsd-3-clause | 3,569 | [
"Galaxy"
] | 50d3ef922519800cd1ca20860cb83b0748e068b8c14828712b9681e1f1c07332 |
"""A kernel manager relating notebooks and kernels
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2013 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, distribu... | WillisXChen/django-oscar | oscar/lib/python2.7/site-packages/IPython/html/services/kernels/kernelmanager.py | Python | bsd-3-clause | 4,895 | [
"Brian"
] | 8ef2fd63c9f2cb450ceaf5ce51ae0350b9e84d2a80416d224649dce64aa22271 |
#!/usr/bin/python
#
# Copyright 2007 Google Inc.
# Licensed to PSF under a Contributor Agreement.
#
# 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... | nouiz/fredericbastien-ipaddr-py-speed-up | tags/2.1.4/ipaddr_test.py | Python | apache-2.0 | 46,220 | [
"FEFF"
] | 83f67b0b1cd7abb7dd680733d4dd78cfa0d2eb0896aec30dd0d1433e855e5e2d |
import numpy as np
from .._common import in_search_space
from .._helpers import SampleResult, register
__all__ = [
"sample",
]
def sample(
fun,
bounds,
x0=None,
args=(),
maxiter=100,
stepsize=0.1,
perc=1.0,
seed=None,
constraints=None,
return_all=True,
callback=None,
... | keurfonluu/StochOPy | stochopy/sample/mcmc/_mcmc.py | Python | mit | 5,627 | [
"Gaussian"
] | f22810b275734e8de972a7a2665eb254638aac36cf967a8a4e897189ef1433bc |
import sys
from time import time
import pandas as pd
from pandas import DataFrame
import numpy as np
import matplotlib.pyplot as plt
import itertools
import matplotlib as mpl
from scipy import linalg
from sklearn import metrics
from sklearn.cluster import KMeans
from sklearn.decomposition import PCA
from sklearn.prep... | avroshk/7100_Spring_16 | Dataset/create/cluster.py | Python | mit | 9,309 | [
"Gaussian"
] | ae2484527cf78f0a3854d0f3290da8181e36e3dd2fa4e7e873300d013c4cecb3 |
##############################################################################
# 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... | matthiasdiener/spack | var/spack/repos/builtin/packages/opencv/package.py | Python | lgpl-2.1 | 14,977 | [
"VTK"
] | 55907b4da11759748f701c3ddd9c3b1819a0ac07e31c630347766ff8856c892c |
# Copyright 2012 Hewlett-Packard Development Company, L.P.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicabl... | jianghuaw/nova | nova/tests/unit/policy_fixture.py | Python | apache-2.0 | 4,663 | [
"TINKER"
] | 3e396c9a3d677e66a0f84516568f70eed09664ef1240bbc5894114baa5b96923 |
#!/usr/bin/env python
"""Run signal-to-reference alignments
"""
from __future__ import print_function
import sys
from signalAlignLib import *
from multiprocessing import Process, Queue, current_process, Manager
from serviceCourse.file_handlers import FolderHandler
from argparse import ArgumentParser
from random import ... | ArtRand/signalAlign | scripts/runSignalAlign.py | Python | mit | 10,710 | [
"BWA"
] | cf16e8df3f6191079f87bfa5c1d7e2d5dca83401c18014157e83f60888ca6b34 |
# -*- coding: utf-8 -*-
"""
Created on Wed Feb 17 18:15:40 2016
@author: Radu
"""
import struct
from neuron import h
def get_net_params(tempdata_address):
text_file_location = tempdata_address + "cell_params"
result = []
text_file = open(text_file_location, 'rb')
value = text_file.read(8)
while ... | penguinscontrol/Spinal-Cord-Modeling | Python/helper_functions.py | Python | gpl-2.0 | 1,497 | [
"NEURON"
] | d2ff23f43385ab178fd8d7fb650416f389418ce7e1120bb0ac2aa32700921898 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements a neutron diffraction (ND) pattern calculator.
"""
import json
import os
from math import asin, cos, degrees, pi, radians, sin
import numpy as np
from pymatgen.symmetry.analyzer import SpacegroupA... | materialsproject/pymatgen | pymatgen/analysis/diffraction/neutron.py | Python | mit | 7,907 | [
"CRYSTAL",
"pymatgen"
] | 81bb81cffab3890a18756af1add32db67e82bfa8ff47c002f61175aa2834b0e3 |
#!/bin/env python
#------------------------------------------------------------------------
# Copyright (c) 1998 by Total Control Software
# All Rights Reserved
#------------------------------------------------------------------------
#
# Module Name: fcgi.py
#
# Description: Han... | MorusAB/commonlib-fmg | pylib/fcgi.py | Python | agpl-3.0 | 14,933 | [
"TINKER"
] | f96be199958ed4dd3695af651fc4117f19cc5561ce190b52b14ee7815c536691 |
# coding: utf-8
# In[1]:
import iris
from iris.unit import Unit
from iris.cube import CubeList
from iris.exceptions import CoordinateNotFoundError, CoordinateMultiDimError
iris.FUTURE.netcdf_promote = True
iris.FUTURE.cell_datetime_objects = True
def time_coord(cube):
"""Return the variable attached to time a... | rsignell-usgs/notebook | iris_snippets.py | Python | mit | 6,452 | [
"ESPResSo"
] | a72251377092f5b2e477711bd06bade74479d0222391a35d421473b8e3acf908 |
'''
Created on 19/02/2010
@author: jose
'''
# Copyright 2009 Jose Blanca, Peio Ziarsolo, COMAV-Univ. Politecnica Valencia
# This file is part of franklin.
# franklin is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Softwar... | JoseBlanca/franklin | franklin/snv/snv_filters.py | Python | agpl-3.0 | 29,261 | [
"BLAST"
] | ba0a81f197b7b37be82d4c0517ac05f3d0ae21492412ecc996167831123066ab |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | harterj/moose | test/tests/outputs/format/test_json.py | Python | lgpl-2.1 | 8,093 | [
"MOOSE"
] | b48882686fe68e8543cd8fca8d06253353052c63e5f50494f85b519630f014e4 |
from yambopy import *
from qepy import *
from schedulerpy import *
import os
import subprocess
from glob import glob
from copy import deepcopy
import matplotlib.pyplot as plt
class YamboDG_Optimize():
"""
Class to generate and run convergence tests for the yambo double grid.
** This class is useful ... | alexmoratalla/yambopy | yambopy/double_grid/dg_convergence.py | Python | bsd-3-clause | 29,787 | [
"CRYSTAL",
"Quantum ESPRESSO",
"Yambo"
] | 1140029a67465f8a7a21374fe0eafb3922e9d6dbd46440d9cab9de4eb249d965 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
dimensions = 1
halfSize1d = 55
GRIDSIZE = [2**12]
halfSize = [halfSize1d,0.1,0.1]# must be three components, because yade is inherently 3D and uses Vector3r. Remaining components will be used for AABB
dampMarginBandMin = 2
dampMarginBandMax = 20
dampFormulaSmooth = Tr... | cosurgi/trunk | examples/qm/1d-free-propagation-DAMP-TEST.py | Python | gpl-2.0 | 6,342 | [
"Gaussian"
] | 8c868212ea19a873ef9788886f4f8a19ddbd19ac9056e3ba54ec2d1461a31556 |
"""
.. module:: compute_month_anomaly.py
:synopsis: This script should calculate the anomaly for every month and
store it as nc files in the appropriate directories.
.. moduleauthor:: Arulalan.T <arulalant@gmail.com>
"""
import os
import sys
import cdms2
# setting the absolute path of the previous di... | arulalant/mmDiagnosis | diagnosis1/diagnosis/compute_month_anomaly.py | Python | gpl-3.0 | 16,848 | [
"NetCDF"
] | b93f5125d8d60057c304f0591c8039f1aaa13c2060a2ef3d721df0360561e554 |
"""
Extract Surface
~~~~~~~~~~~~~~~
You can extract the surface of nearly any object within ``pyvista``
using the ``extract_surface`` filter.
"""
# sphinx_gallery_thumbnail_number = 2
import numpy as np
import pyvista as pv
from vtk import VTK_QUADRATIC_HEXAHEDRON
###################################################... | akaszynski/vtkInterface | examples/01-filter/extract-surface.py | Python | mit | 2,740 | [
"VTK"
] | ab410f0ae8209bf6d506c3a86be4684e0608af2fa192c4785e5fafa0978ea044 |
""" @package antlr3.tree
@brief ANTLR3 runtime package, treewizard module
A utility module to create ASTs at runtime.
See <http://www.antlr.org/wiki/display/~admin/2007/07/02/Exploring+Concept+of+TreeWizard> for an overview. Note that the API of the Python implementation is slightly different.
"""
# begin[licence]
#... | ychen820/microblog | y/google-cloud-sdk/platform/google_appengine/lib/antlr3/antlr3/treewizard.py | Python | bsd-3-clause | 18,202 | [
"VisIt"
] | 288e596f72c11952e10eb78743d2ed7ae0a5008797fade93495f26cd33c02c27 |
""" Create and send a combined request for any pending operations at
the end of a job:
* fileReport (for the transformation)
* jobReport (for jobs)
* accounting
* request (for failover)
"""
from DIRAC import gLogger
from DIRAC.Workflow.Modules.ModuleBase impor... | arrabito/DIRAC | Workflow/Modules/FailoverRequest.py | Python | gpl-3.0 | 3,764 | [
"DIRAC"
] | fa9dfc1a2cfd63a8f97976364256017086b64649344c376c4ec0ce0d682df97a |
"""
:mod:`bein` -- LIMS and workflow manager for bioinformatics
===========================================================
.. module:: bein
:platform: Unix
:synopsis: Workflow and provenance manager for bioinformatics
.. moduleauthor:: BBCF <webmaster.bbcf@epfl.ch>
Bein contains a miniature LIMS (Laboratory In... | bbcf/bbcflib | bein/__init__.py | Python | gpl-3.0 | 70,402 | [
"Galaxy"
] | 9043f7dc0cb6fa89ad4003d66c7c56b03145ee3f9557d2ecd526e7166cb4372b |
# -*- coding: utf-8 -*-
import collections
import gzip
import itertools
import io
import logging
import math
import re
import sys
import matplotlib
matplotlib.use('agg')
import matplotlib.pyplot as plt
plt.switch_backend('agg')
import numpy as np
import seaborn as sns
from .amino_acids import _SUBSTITUTION_MATRICES... | vlopezferrando/pymut | pymut/features.py | Python | mit | 22,474 | [
"BLAST"
] | 253c7aabb40c6c5baa7990a218dbd06c40fa45b54a04d89b69e1f2cd63e9f951 |
from setuptools import setup
from terminus.version import version_str
setup(
name='terminus',
version=version_str,
author='Brian Cline',
author_email='brian.cline@gmail.com',
description=('Updates interfaces file on Debian Linux-based distros'),
long_description=open('README.rst').read(),
l... | briancline/terminus | setup.py | Python | mit | 933 | [
"Brian"
] | 99329be4e69757a95baa39ed0765eccd0aa3372bb0e192d26fbc3ef9e9091977 |
import os
import unittest
import tensorflow as tf
from pymatgen.core import Molecule
from megnet.models import MEGNetModel
from megnet.utils.molecule import get_pmg_mol_from_smiles, pb
CWD = os.path.dirname(os.path.abspath(__file__))
class TestMolecule(unittest.TestCase):
@classmethod
def setUpClass(cls):
... | materialsvirtuallab/megnet | megnet/utils/tests/test_molecule_util.py | Python | bsd-3-clause | 917 | [
"pymatgen"
] | 43234df2db0514be0dee348d9ca43922fed294ea3ef88d27f4756ec8826ba6b4 |
##
# Copyright 2009-2012 Ghent University
# Copyright 2009-2012 Stijn De Weirdt
# Copyright 2010 Dries Verdegem
# Copyright 2010-2012 Kenneth Hoste
# Copyright 2011 Pieter De Baets
# Copyright 2011-2012 Jens Timmerman
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://u... | JensTimmerman/easybuild-easyblocks | easybuild/easyblocks/l/libsmm.py | Python | gpl-2.0 | 8,618 | [
"CP2K"
] | 5cb3c61b5813789094dd57d3e3a0bbacd8b5d79f59578ab9202d4b9d89a1aa0d |
# -*- coding: utf-8 -*-
"""
Created on Sat Feb 6 22:24:26 2016
@author: david
"""
# This is a configuration step for the exercise. Please run it before calculating the derivative!
import numpy as np
import matplotlib.pyplot as plt
# Function for setting up the Chebyshev derivative matrix
def get_cheby_matrix(nx):
... | davofis/computational_seismology | 05_pseudospectral/cheby_derivative.py | Python | gpl-3.0 | 1,828 | [
"Gaussian"
] | cb1f318641a81180b944f10c351f8557c8c622935f194e8b12972987bfef8b04 |
# -*- coding: utf-8 -*-
#------------------------------------------------------------
# pelisalacarta - XBMC Plugin
# Canal para yaske
# http://blog.tvalacarta.info/plugin-xbmc/pelisalacarta/
#------------------------------------------------------------
import urlparse,urllib2,urllib,re
import os, sys
from core import... | golaizola/pelisalacarta-xbmc | pelisalacarta/channels/yaske.py | Python | gpl-3.0 | 14,531 | [
"ADF"
] | b5e49c060db5c7cfcc7983c096ba81b1f2b582336c839349cd1dc08e41e8ce98 |
from ddt import ddt, data, unpack
from .base_test import MentoringBaseTest
CORRECT, INCORRECT, PARTIAL = "correct", "incorrect", "partially-correct"
@ddt
class MentoringAssessmentTest(MentoringBaseTest):
def _selenium_bug_workaround_scroll_to(self, mentoring):
"""Workaround for selenium bug:
Som... | open-craft/xblock-mentoring | tests/integration/test_assessment.py | Python | agpl-3.0 | 16,811 | [
"VisIt"
] | ac64306d39b0f2bdeb6720e0c395a8510e04dfb7462619422a5b29dd8a479da2 |
from __future__ import absolute_import, division, print_function
import numpy as np
from numpy import (
sqrt,
minimum,
)
try:
_ = np.use_fastnumpy # Use Enthought MKL optimizations
from numpy.fft import rfft, irfft, rfftfreq
except AttributeError:
try:
import mklfft # MKL FFT optimization... | achabotl/pambox | pambox/central/ec.py | Python | bsd-3-clause | 17,944 | [
"Gaussian"
] | a914bac3128c4fc723332d99c65201bc0ea6f80a5a0f3c500240366a17a21fc3 |
#!/usr/bin/env python
#20-11-2017
#Authors:Sebastian ECHEVERRI RESTREPO,
# sebastian.echeverri.restrepo@skf.com, sebastianecheverrir@gmail.com
# James EWEN
# j.ewen14@imperial.ac.uk, jimmyewen@gmail.com
#################################################################################3
#Appart from generating the... | JE1314/LAMMPS_builder | root/AddFe2O3.py | Python | gpl-3.0 | 4,567 | [
"LAMMPS"
] | dde6d0c124361da746d0691f1282eef3ced63c7ee3e7738a07d2d3cd02ab1aba |
"""Configure file for PyMorph. Authors: Vinu Vikram, Yogesh Wadadekar and Ajit Kembhavi 2008"""
###----Specify the input images and Catalogues----###
imagefile = '00000002_r_stamp.fits'
whtfile = '00000002_r__r_W.fits' #The weight image. If it contains the
#string 'rms', this wi... | vvinuv/pymorph | test_data/config.py | Python | gpl-2.0 | 5,699 | [
"Galaxy"
] | b72459e197f4254d6b3df3a1bfb51082789d167e40d498575313fa45ba0a2928 |
import pysam
import csv
import sys
import collections
class Variant(object):
def __init__(self, original, new, refdict):
self.original = original
self.new = new
self.chrom = self.original['CHROM']
self.position = int(self.original['POS'])
self.coordinates = (self.chrom, se... | d-quinn/bio_quinn2013 | SNP_calling/no_filter/snps_combine.py | Python | mit | 8,790 | [
"pysam"
] | 7dc2d291ab7d8f72e878ae0182bcc1ff03fd36ac8b12d94f965ed6e55b6831f9 |
# minimal.py ---
# Upi Bhalla, NCBS Bangalore 2014.
#
# Commentary:
#
# Minimal model for loading rdesigneur: reac-diff elec signaling in neurons
#
# 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 Founda... | dilawar/moose-full | moose-examples/snippets/MULTI/minchan.py | Python | gpl-2.0 | 12,176 | [
"MOOSE"
] | 75d899272449ed9e587207b896ecb0d3befb78c3eff608d5fba18a9ae71e6265 |
"""
Tests i18n in courseware
"""
import re
from nose.plugins.attrib import attr
from django.conf import settings
from django.contrib.auth.models import User
from django.core.urlresolvers import reverse, NoReverseMatch
from django.test import TestCase
from django.test.client import Client
from django.utils import trans... | Learningtribes/edx-platform | lms/djangoapps/courseware/tests/test_i18n.py | Python | agpl-3.0 | 8,118 | [
"VisIt"
] | 15127ccc304ac67a8b482547b1005506ac48166d9d48b9029c3429e45bea7057 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | jensreeder/scikit-bio | skbio/util/tests/test_misc.py | Python | bsd-3-clause | 10,757 | [
"scikit-bio"
] | 90f730608ef2b847d609ec5fb2a1fe5fc720c7ac828eb02990f7a08b9389d8d4 |
# 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 abc
import re
import os
import glob
import shutil
import warnings
from itertools import chain
from copy import deepcopy
import six
impo... | xhqu1981/pymatgen | pymatgen/io/vasp/sets.py | Python | mit | 58,868 | [
"VASP",
"pymatgen"
] | 8c9f70f6e7d482d74e1facf70138e9411d97467ae7cf10038122bf1c83d4bbe5 |
# -*- coding: utf-8 -*-
#
# Author: Taylor Smith <taylor.smith@alkaline-ml.com>
#
# Common ARIMA functions
from sklearn.utils.validation import column_or_1d
import numpy as np
import warnings
from .. import context_managers as ctx
from ..utils import get_callable
from ..utils.array import diff, check_endog
from ..co... | tgsmith61591/pyramid | pmdarima/arima/utils.py | Python | mit | 6,450 | [
"ADF"
] | 5ce17556bca869f8cc59407a9e202a5961c44134e328d7028e859d794ea5f5e6 |
# Copyright 2014 PerfKitBenchmarker Authors. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appli... | akshara775/PerfKitBenchmarker-master-2 | perfkitbenchmarker/linux_benchmarks/cassandra_stress_benchmark.py | Python | apache-2.0 | 20,941 | [
"Gaussian"
] | 7f509f57e6be959aeb67aa04f11b8be1f54fa5f8e6c913a7c56d57ba476dc412 |
# coding: utf8
{
' Module is the main communications hub of the Sahana system. It is used to send alerts and/or messages using SMS & Email to various groups and individuals before, during and after a disaster.': ' Module is the main communications hub of the Sahana system. It is used to send alerts and/or messages us... | ksetyadi/Sahana-Eden | languages/ur.py | Python | mit | 228,256 | [
"VisIt"
] | ac882c75737ee58aa02ac3a95994e29ac3aa75c8e036ef3c03e255d3268e3455 |
# import vtk wrapped version that will raise exceptions for error events
import vtkwithexceptions as vtk
import base64
import os
import tempfile
from celery import Celery
from celery import task, current_task
from celery.result import AsyncResult
from visomics.vtk.common import parse_json
celery = Celery()
celery.co... | Visomics/Visomics | AnalysisServer/visomics/vtk/r.py | Python | apache-2.0 | 4,173 | [
"VTK"
] | aca3c76d8c60cd5c5ce9f26c30369d5755ccbf8f919d495b22582ceec99fde51 |
# -*- coding: utf-8 -*-
#
# Copyright © 2013 Michael Rabbitt.
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation the rights to use, copy, mo... | getnikola/nikola | nikola/plugins/compile/markdown/mdx_gist.py | Python | mit | 6,603 | [
"Brian"
] | 5ff66fe292b49b57c1fb45c0b577f42cd38920f393d02c09ca0bc4acd5f76828 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements methods for writing LAMMPS input files.
"""
import os
import re
import shutil
import warnings
from string import Template
from monty.json import MSONable
from pymatgen.io.lammps.data import Lammp... | vorwerkc/pymatgen | pymatgen/io/lammps/inputs.py | Python | mit | 7,388 | [
"LAMMPS",
"pymatgen"
] | 1f24afa7a4d90a40e74ccf880bcb5d0670c85a098f3f26d28810f95ed767826f |
# Hidden Markov Models
#
# Author: Ron Weiss <ronweiss@gmail.com>
# and Shiqiao Du <lucidfrontier.45@gmail.com>
# API changes: Jaques Grobler <jaquesgrobler@gmail.com>
"""
The :mod:`sklearn.hmm` module implements hidden Markov models.
**Warning:** :mod:`sklearn.hmm` is orphaned, undocumented and has known
numerical s... | chaluemwut/fbserver | venv/lib/python2.7/site-packages/sklearn/hmm.py | Python | apache-2.0 | 48,579 | [
"Gaussian"
] | 83b3306da180c3c33024c0c04a504fc6c7a471ca8037256697ed23703f426fef |
import unittest
from DIRAC.Core.Workflow.Module import ModuleDefinition
from DIRAC.Core.Workflow.Step import StepDefinition
from DIRAC.Interfaces.API.Job import Job
from DIRAC.Workflow.Utilities.Utils import getStepDefinition, getStepCPUTimes
###########################################################################... | avedaee/DIRAC | Workflow/Utilities/test/Test_Utilities.py | Python | gpl-3.0 | 2,812 | [
"DIRAC"
] | a3257f2498a891b32b9738b014994653e71aea3ab99f392cc6c9a41b9045cd68 |
import unittest
from test import test_support
from itertools import *
from weakref import proxy
import sys
import operator
import random
maxsize = test_support.MAX_Py_ssize_t
minsize = -maxsize-1
def onearg(x):
'Test function of one argument'
return 2*x
def errfunc(*args):
'Test function that raises an er... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-2.6/Lib/test/test_itertools.py | Python | mit | 52,962 | [
"GULP"
] | 83ac248e5ca0bc6fd05f497cba63d7d6e8aa5e3a14da72d51031e735feaf4020 |
#!/usr/bin/env python
#29-11-2016
#Authors:Sebastian ECHEVERRI RESTREPO,
# sebastian.echeverri.restrepo@skf.com, sebastianecheverrir@gmail.com
# James EWEN
# j.ewen14@imperial.ac.uk, jimmyewen@gmail.com
#################################################################################3
# This file adds the info... | JE1314/LAMMPS_builder | root/AddEAM.py | Python | gpl-3.0 | 2,700 | [
"LAMMPS"
] | 81085b8db0b22d5c8cc31b65f78abbbb07281477aa7182604e3483942a4bfdb6 |
#!/usr/bin/python
# File: Psycollider.py
# Copyright (c) Benjamin Golinvaux
#
# 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 2 of the
# License, or (at your option) any later... | GameOfLife/WFSCollider | editors/Psycollider/Psycollider.py | Python | gpl-3.0 | 60,560 | [
"VisIt"
] | caed73179b87bd8d16e515b313caab28140acc3d76f40ab4a1a195e10e5306fd |
"""
Downloads feeds, keys, packages and icons.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _, logger
import os, sys
from zeroinstall import support
from zeroinstall.support import tasks, basedir, portable_rename
from zeroinstall.in... | linuxmidhun/0install | zeroinstall/injector/fetch.py | Python | lgpl-2.1 | 31,332 | [
"VisIt"
] | a4a6dc050d92cc8630a84a9bd782d3a23008c364864cb321f3f4d66d9af0860d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
Created on Tue Oct 27 15:59:28 2015
@author: dominic
"""
###############################################################################
# Blast Functions #############################################################
#######################################################... | DJBAR/SNPfinder | SNPfinder.py | Python | gpl-2.0 | 23,524 | [
"BLAST"
] | 64c0bffcebc786617ce26c283e2ab14168f235262663cda0009dc5ef5012e852 |
#!/usr/bin/env python
import os
import sys
import subprocess
from setuptools import setup, find_packages
subprocess.call(
('mkdir -p seqmagick/data && '
'git describe --tags --dirty > seqmagick/data/ver.tmp '
'&& mv seqmagick/data/ver.tmp seqmagick/data/ver '
'|| rm -f seqmagick/data/ver.tmp'),
... | fhcrc/seqmagick | setup.py | Python | gpl-3.0 | 1,667 | [
"Biopython"
] | d84de71120117ab97aef7a6562dbe9c55fc0a529bbca84db7430de2e8dc036bc |
# -*- coding: utf-8 -*-
# this file is released under public domain and you can use without limitations
#########################################################################
## This is a sample controller
## - index is the default action of any application
## - user is required for authentication and authorization... | prateekgupta3991/justforlearn | controllers/reconciliotastic.py | Python | mit | 6,674 | [
"Biopython"
] | badcaa102681ac436d415eec39374775a17c0f6b700a5df63b3bd7855750dfaa |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/postprocessing/combine_csv.py | Python | lgpl-2.1 | 8,745 | [
"MOOSE"
] | a07f11474a5b6d8ef1b5197627b29ab576f38eafff657cfe799fbb60889fbba0 |
# sybase/base.py
# Copyright (C) 2010-2021 the SQLAlchemy authors and contributors
# <see AUTHORS file>
# get_select_precolumns(), limit_clause() implementation
# copyright (C) 2007 Fisch Asset Management
# AG https://www.fam.ch, with coding by Alexander Houben
# alexander.houben@thor-solutions.ch
#
# This module is pa... | monetate/sqlalchemy | lib/sqlalchemy/dialects/sybase/base.py | Python | mit | 32,421 | [
"ASE"
] | 79307c618266e6237ee767b75fcf7349f5c693f6fa4d58dbac13122608eb6305 |
#
# Evy - a concurrent networking library for Python
#
# Unless otherwise noted, the files in Evy are under the following MIT license:
#
# Copyright (c) 2012, Alvaro Saurin
# Copyright (c) 2008-2010, Eventlet Contributors (see AUTHORS)
# Copyright (c) 2007-2010, Linden Research, Inc.
# Copyright (c) 2005-2006, Bob Ippo... | inercia/evy | evy/event.py | Python | mit | 10,576 | [
"VisIt"
] | b79327337a393e315421a6c5e2bf076d726a409c25cab7fd833ce8e598c2fe61 |
#
# Copyright 2018 Red Hat | Ansible
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# ... | skg-net/ansible | lib/ansible/utils/module_docs_fragments/k8s_auth_options.py | Python | gpl-3.0 | 2,834 | [
"VisIt"
] | fc4aa8f2563a8315d38c9b360c9d9e687bc34b02c79172189f00bdf717f54430 |
##############################################################################
# Copyright (c) 2013-2017, 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... | skosukhin/spack | var/spack/repos/builtin/packages/r-a4/package.py | Python | lgpl-2.1 | 1,915 | [
"Bioconductor"
] | e85db38c4a93367b1a2e1102a78c8ae1128ef451de27eabe6a52d04b9ba262e5 |
# Copyright (C) 2014-2016 DNAnexus, Inc.
#
# This file is part of dx-toolkit (DNAnexus platform client libraries).
#
# 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.a... | dnanexus/dx-toolkit | src/python/dxpy/utils/file_load_utils.py | Python | apache-2.0 | 15,802 | [
"BWA"
] | 0ee115e42bfa913cb8d06302e9cd8a6fb4e7391b29cb9295933b4c99d0f8ed5d |
# nsdf.py ---
#
# Filename: nsdf.py
# Description:
# Author: subha
# Maintainer:
# Created: Fri Jun 26 12:23:07 2015 (-0400)
# Version:
# Last-Updated: Tue Dec 29 12:50:27 2015 (-0500)
# By: Subhasis Ray
# Update #: 6
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
# __BROKEN__
#
#
#
# Change log:... | BhallaLab/moose-examples | snippets/nsdf.py | Python | gpl-2.0 | 6,010 | [
"MOOSE"
] | 87ab7c0b314fea9f976d3789f8faa1ad6fb394c01093f18124e67469f6f1d6ec |
# Orca
#
# Copyright 2005-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | chrys87/orca-beep | src/orca/keybindings.py | Python | lgpl-2.1 | 17,431 | [
"ORCA"
] | 48815ba6c7f6bc43650cf9f4274859658543f272e709a80f5b2f65f24744f348 |
###########################################################################
# (C) 2016 Elettra - Sincrotrone Trieste S.C.p.A.. All rights reserved. #
# #
# #
# This file is ... | ElettraSciComp/STP-Core | STP-Core/preview_reconstruct.py | Python | gpl-3.0 | 23,605 | [
"Gaussian"
] | ac90849f85af2125a58953a8ab6f0badacf27aa774fed7fa098f0761a9edd492 |
import json
import numpy as np
import os
from itertools import groupby
from operator import itemgetter
import copy
import sys
from finisherSCCoreLib import alignerRobot
from finisherSCCoreLib import graphLib
from finisherSCCoreLib import IORobot
from finisherSCCoreLib import houseKeeper
import associatedReadFinder
im... | kakitone/finishingTool | experimental/abunSplitter.py | Python | mit | 11,578 | [
"Bowtie"
] | 18e3c3fa04b8d0bf94847899765215d3d7b2c2304b81301708b36de7846d4f2a |
# Copyright 2006-2010 by Peter Cock. 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.
#
#Nice link:
# http://www.ebi.ac.uk/help/formats_frame.html
"""Sequence input/output as Seq... | ktokolwiek/Genetic-Stability-Tool | Bio/SeqIO/__init__.py | Python | gpl-3.0 | 34,823 | [
"BioPerl",
"Biopython"
] | 2e611a9292b5e58e06c9b6be556bebd1ddea4b3cc60d9d3692ec9edf5763655b |
#!/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... | squeed/kubernetes | cluster/juju/layers/kubernetes-worker/reactive/kubernetes_worker.py | Python | apache-2.0 | 37,815 | [
"CDK"
] | 25096878ae938c16493fca0a8560cb18f0eb2cab5f1bc4a6c2a6fe572923a0ba |
# antlr4_tex2sym.py Author: Akira Hakuta, Date: 2019/04/05
# python.exe antlr4_tex2sym.py
import sys
import antlr4
from gen.TeX2SymLexer import TeX2SymLexer
from gen.TeX2SymParser import TeX2SymParser
from gen.TeX2SymVisitor import TeX2SymVisitor
from sympy import *
# variable : a,b,...,z, A,B,..,Z, \\alpha, \\be... | AkiraHakuta/antlr4_tex2sym | antlr4_tex2sym.py | Python | mit | 11,716 | [
"VisIt"
] | 2c102f54a7754a5fd28650ad50a650d172c4ced20dcd799b86c6ee4d69c29e60 |
import fokabot
import random
import glob
import serverPackets
import exceptions
import userHelper
import time
import systemHelper
"""
Commands callbacks
Must have fro, chan and messages as arguments
fro -- name of who triggered the command
chan -- channel where the message was sent
message -- list containing argumen... | osuripple/ripple | c.ppy.sh/fokabotCommands.py | Python | mit | 10,048 | [
"MOE"
] | f61dadfdb47a54e742afd9a8ae59a0e9cadef9d3dfc732207e73d60e313be689 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
A couple of helper functions for doing numpy-like stuff with numpy.
"""
from mathics.core.expression import Expression
from functools import reduce
import numpy
import ast
import inspect
import sys
#
# INTERNAL FUNCTIONS
#
def _promote(x, shape):
if isinstance(... | pqtoan/mathics | mathics/builtin/numpy_utils/with_numpy.py | Python | gpl-3.0 | 12,764 | [
"VisIt"
] | 9879e104bda221c61f83fa42f84492d16a17769824310af6a93d0b889434aec7 |
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