text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
# vim: ts=4 sw=4 expandtab
""" This is an abstract module for visiting specific nodes. This is useed to
traverse the tree to generate warnings.
"""
def visit(event, *args):
""" This decorator is used to indicate which nodes the function should
examine. The function should accept (self, node) and return the rel... | melloc/javascriptlint | javascriptlint/visitation.py | Python | gpl-2.0 | 1,893 | [
"VisIt"
] | a3fd8e7aba2319b280cadc9ea2996e104263a7ec069a86c9909cfeff84785f37 |
from __future__ import print_function
import contextlib
from distutils.command import build_ext, build_py
from distutils.core import setup, Command
from distutils.sysconfig import get_config_var
from distutils.util import convert_path
import fnmatch
import multiprocessing
import os
import sys
import numpy as np
impor... | mo-g/iris | setup.py | Python | gpl-3.0 | 7,008 | [
"NetCDF"
] | 5706f2cf56bceecee1da502ad0dad555ef5757962ea70e688a17f27cd8bc3a84 |
# -*- coding: utf-8 -*-
# (c) Nelen & Schuurmans. GPL licensed, see LICENSE.rst.
""" TODO Docstring. """
import argparse
import logging
import sys
import h5py
import numpy as np
from PIL import Image
from matplotlib import colors
from matplotlib import cm
from openradar import calc
from openradar import config
lo... | nens/openradar | openradar/scripts/elevation_image.py | Python | gpl-3.0 | 2,413 | [
"ASE"
] | c70b75f991064f80328abf2b84aec30d7b6a86baf0f184c05be4a54ee610d586 |
# -*- coding: utf-8 -*-
'''Graphic representation of fields over the mesh.'''
__author__= "Luis C. Pérez Tato (LCPT) , Ana Ortega (AO_O) "
__copyright__= "Copyright 2016, LCPT, AO_O"
__license__= "GPL"
__version__= "3.0"
__email__= "l.pereztato@ciccp.es, ana.ortega@ciccp.es "
import vtk
from miscUtils import LogMes... | lcpt/xc | python_modules/postprocess/xcVtk/FE_model/Fields.py | Python | gpl-3.0 | 4,928 | [
"VTK"
] | 6c77d0bbae494200b7f141d576b8501fe2c745e97c9ac31e7700ac68b0def288 |
import math
import numpy as np
class NoisePower(object):
"""This class holds static methods used to calculate noise
"""
@staticmethod
def cutoff_power_correction(raw_data):
"""Computes the correction factor for noise power
Computes a correction factor for the noise. Without this
... | SuperDARNCanada/backscatter | backscatter/fitacf/noisepower.py | Python | gpl-3.0 | 2,326 | [
"Gaussian"
] | 64516626315b1b2b92293596eafea3caf7045ba78e3b7b1451d398d579437649 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
## all SI units
########################################################################################
## Plot the firing rate vs current injection curve for a Cerebellar Granule Cell neuron
## Author: Aditya Gilra
## Creation Date: 2012-07-12
## Modification Date: 2012-07-12... | h-mayorquin/camp_india_2016 | tutorials/chemical switches/moose/neuroml/GranuleCell/FvsI_Granule98.py | Python | mit | 2,307 | [
"MOOSE",
"NEURON"
] | 8f2886a649dc1850700440e5e618ac10de5ef5f69c5cb51753543d3c37f003e4 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | psci2195/espresso-ffans | src/python/espressomd/observables.py | Python | gpl-3.0 | 21,923 | [
"ESPResSo"
] | ce766b3f011e1009cd51c5b414bc3bb7acd5440ff6f27ac585a5f2c4f70860fa |
"""
conversion/neuromlFormat.py
Contains functions related to neuroml conversion (import from and export to)
Contributors: salvadordura@gmail.com
"""
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
from builtins import str
from builtins import range
t... | thekerrlab/netpyne | netpyne/conversion/neuromlFormat.py | Python | mit | 74,537 | [
"NEURON",
"VisIt"
] | 94669b32443124e3fc61ec5ed8139b6e63bbb038b66358c4b7152fbff548497a |
# Copyright 2014 Roberto Brian Sarrionandia
#
# 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 t... | sarrionandia/tournatrack | tab.py | Python | apache-2.0 | 2,023 | [
"Brian"
] | 3286f461c34e9b193e336435ccccd1a7ee9c525c08b6c87daae1e6f3a7714c08 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | annarev/tensorflow | tensorflow/python/autograph/pyct/qual_names.py | Python | apache-2.0 | 8,385 | [
"VisIt"
] | f34bf80e7053e5a9e883ab7983c6796570accfc940d8c6f3e05cf67b356cedad |
# -*- coding: utf-8 -
"""
Authors: David Kent, Tim Bedin, Tim Erwin
Copyright 2014 CSIRO
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 ... | taerwin/cwsl-mas | cwsl/core/scheduler.py | Python | apache-2.0 | 7,142 | [
"NetCDF"
] | 57b34032ce81461dca738a11d75e2ed4eb1c57002d78c6f019479d1c63ec3b1b |
#!/usr/bin/env python
from __future__ import division, print_function #, unicode_literals
import os
import sys
import time
from subprocess import Popen
from .subprocesswithtimeout import SubProcessWithTimeout
try:
from ConfigParser import SafeConfigParser, NoOptionError
except ImportError:
# The ConfigParser... | SamKChang/abinit-7.10.5_multipole | tests/pymods/jobrunner.py | Python | gpl-3.0 | 18,759 | [
"ABINIT"
] | 58ef49556eedb47980aabfeccbec96f571230c570661be2c595ef11f71867846 |
def pickleTraj(TrajName, LogFile = None, LogFileToken = None, Verbose = False):
import os, cPickle as pickle
import sim
pickleName = TrajName + '.pickle'
if os.path.isfile(pickleName):
of = open(pickleName, 'r')
if Verbose: print 'Loading from pickle...'
Trj = pickle.load(of... | tanmoy7989/mysim | pickleTraj.py | Python | gpl-3.0 | 702 | [
"LAMMPS"
] | 4da12a55a2f3ef653185708d3681c47b1ec21e73aa0057b98719f63b5274a6c9 |
#!/usr/bin/env python
# polarizer.py - add Drude oscillators to LAMMPS data file.
# Agilio Padua <agilio.padua@univ-bpclermont.fr>
# Alain Dequidt <alain.dequidt@univ-bpclermont.fr>
# version 2017/02/08
import sys
import argparse
import random
from copy import deepcopy
usage = """Add Drude oscillators to LAMMPS data ... | rbberger/lammps | tools/drude/polarizer.py | Python | gpl-2.0 | 28,462 | [
"LAMMPS"
] | 0ca32ce0803c1ed213837d56dfc57c40a03cbea0263f5f0c83dfae152f0d5911 |
from matplotlib import pyplot as plt
import warnings
with warnings.catch_warnings():
warnings.simplefilter("ignore")
import seaborn as sns
def pkmu_normalization(driver):
"""
Return P(k,mu) normalization, using the current
values of `f` and `b1`, and the properly normalized
no-wiggle linear po... | nickhand/pyRSD | pyRSD/rsdfit/util/plot.py | Python | gpl-3.0 | 7,344 | [
"Galaxy"
] | 68c891611f521d8b7f03f1b119abb3731eaa258f9fdbe88b956f099dddaeb307 |
from __future__ import print_function, division
import random
from sympy import Derivative
from sympy.core.basic import Basic
from sympy.core.compatibility import is_sequence, as_int, range
from sympy.core.function import count_ops
from sympy.core.decorators import call_highest_priority
from sympy.core.singleton impo... | aktech/sympy | sympy/matrices/dense.py | Python | bsd-3-clause | 44,552 | [
"DIRAC"
] | fb313ce0b5897ba841fa0afee0a62eddfba21720bc91c9823210feba48091256 |
class Solution(object):
def dfs(self, v, visit, gr, ans):
if visit[v] == -1:
return False
elif visit[v] == 1:
return True
visit[v] = -1
for i in gr[v]:
if visit[i] == -1 or not self.dfs(i, visit, gr, ans):
return False
an... | quake0day/oj | Course Schedule ii.py | Python | mit | 876 | [
"VisIt"
] | 040b9e4bb3b2a52df7781114e40a09425e933bae78a96ed7aab4addd38bfef0c |
# Copyright (C) 2016
# Jakub Krajniak (jkrajniak at gmail.com)
#
# This file is part of ChemLab.
#
# ChemLab 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... | cgchemlab/chemlab | src/chemlab/files_io.py | Python | gpl-3.0 | 47,994 | [
"Gromacs",
"LAMMPS"
] | ac008e3b4329c78045cacf311cf0d8ab62a1eb3cbac5ce6f3c7f1245e1403b39 |
# Author: Travis Oliphant 2001
# Author: Nathan Woods 2013 (nquad &c)
import sys
import warnings
from functools import partial
from . import _quadpack
import numpy
from numpy import Inf
__all__ = ['quad', 'dblquad', 'tplquad', 'nquad', 'quad_explain',
'IntegrationWarning']
error = _quadpack.error
class ... | person142/scipy | scipy/integrate/quadpack.py | Python | bsd-3-clause | 37,234 | [
"Gaussian"
] | c4af9ee91c5fa05988483a9ca8570d6ed51786420322e7742020ce75a87660cb |
#!/usr/bin/env python
"""
lib.py
Library of utilities for ocean models, imported into the namespace
when importing the model module
Written by Brian Powell on 10/18/13
Copyright (c)2017 University of Hawaii under the BSD-License.
"""
import numpy as np
import seapy
import scipy.constants
# Define reference... | dalepartridge/seapy | model/lib.py | Python | mit | 11,915 | [
"Brian"
] | a57427adfcffb5ed358063768dc966a9dcfe447acb512df816aa3b0f46f9920e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# MODULE IMPORT
from __future__ import print_function
import subprocess
from termcolor import cprint
import fenics as fe
__author__ = "Alessio Nava"
__copyright__ = "2017 Alessio Nava"
__credits__ = ["Alessio Nava, the FEniCS Team"]
__license__ = "GPL"
__version__ = "3.0... | alen12345/nonlinearHyperElasticity | nlhe/solvers/nlhe.py | Python | gpl-3.0 | 7,466 | [
"ParaView",
"VTK"
] | e76fe44965d2728809a1ce6dc6b7b8658736e22c01e5d2a29e428b66ec29a5d7 |
def treePostOrder(root):
if not root:
return
stack = []
node = root
while len(stack) > 0 or node:
if node:
stack.append(node)
node = node.right
else:
node = stack.pop()
#visit node
node = node.left
| urashima9616/Leetcode_Python | BinaryPostOrderTraverse.py | Python | gpl-3.0 | 302 | [
"VisIt"
] | d35bb84f4d7199ca5c655506c26fb363bfbd20da941b7418bf089e217f560b01 |
#########################################################################
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2013 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version 2... | BhallaLab/moose | moose-examples/tutorials/ChemicalBistables/findSteadyState.py | Python | gpl-3.0 | 7,601 | [
"MOOSE"
] | dd152e7f6f06f1171a7a86c0d1dfc9975470a2ac577ca2e1abf6e237c579c235 |
# # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # # #
#
# Okinawa Institute of Science and Technology, Japan.
#
# This script runs on STEPS 2.x http://steps.sourceforge.net
#
# H Anwar, I Hepburn, H Nedelescu, W Chen and E De Schutter
# Stochastic calcium mechanisms cause dendritic calcium spike... | CNS-OIST/STEPS_Example | publication_models/API_1/Anwar_J Neurosci_2013/HybridCaburst_detchannels.py | Python | gpl-2.0 | 27,586 | [
"Avogadro"
] | 9cf2060668cacbba63f6cb90570470f95d777150337ce9428f562f1db2f11380 |
#!/usr/bin/env python
# PythonJS to JavaScript Translator
# by Amirouche Boubekki and Brett Hartshorn - copyright 2013
# License: "New BSD"
import os, sys
from types import GeneratorType
import ast
from ast import Str
from ast import Name
from ast import Tuple
from ast import parse
from ast import Attribute
from ast... | jinankjain/PythonJS | pythonjs/pythonjs.py | Python | bsd-3-clause | 23,317 | [
"VisIt"
] | aaf5e4dff2150da59f98f02b3530fd00f46f758e46a9b4f88102af22acff56ee |
import sfh_tests_multi_proc as sfh_tests
import os
import numpy as np
import matplotlib.pylab as plt
from TPAGBparams import snap_src, research_path
import brewer2mpl
import ResolvedStellarPops as rsp
import fileIO
import galaxy_tests
color_scheme = ['#d73027', '#fc8d59', '#fee090', '#669966', '#e0f3f8', '#4575b4']
f... | philrosenfield/TPAGB-calib | model_plots.py | Python | bsd-3-clause | 26,550 | [
"Gaussian"
] | 37770fc371c85827953ee7f4d004fa3aa67dbe449a0a66d31aa95f651bdb4f3b |
"""Align coordinate to reference, using a fasta alignment to find the
common atoms."""
from staging.SunGridEngine import Job
#from staging.Local import Job
job = Job(inputfiles=dict(sequence='sequences/1IFC_R151IFC.fasta',
ref_psf='coord/1ifc_xtal.psf',
ref_pdb='coo... | iwelland/hop | doc/examples/referenceframe.py | Python | lgpl-3.0 | 1,469 | [
"MDAnalysis"
] | ed6ecce170844725f9e492b6170f8c4c455b48b00916f9d90c723b8aec25d47a |
from __future__ import unicode_literals
import logging
import time
from django.conf import settings
from django.contrib.auth.decorators import login_required
from django.contrib.auth.models import User
from django.contrib.sites.models import Site
from django.core.exceptions import MultipleObjectsReturned, ObjectDoesN... | beol/reviewboard | reviewboard/reviews/views.py | Python | mit | 64,687 | [
"VisIt"
] | 27106aeb0b600b9163b1fbf244332de26f258849c6d969a142b1119385e85e8f |
respuestas = []
numero_personas = int(input())
while numero_personas:
personas = [int(x) for x in input().split()]
anterior = personas[0]
dalton = True
for x in personas[1:]:
dalton = dalton and anterior < x
anterior = x
if dalton:
respuestas.append('DALTON')
else:
... | israelem/aceptaelreto | codes/2018-02-19-dalton.py | Python | mit | 441 | [
"Dalton"
] | dfec6db4cc34d944166b8a9347610941119553b1d38a6b8d549a3eaf070fe8ac |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
FIXME: Proper module docstring
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer... | aykol/pymatgen | pymatgen/util/tests/test_string_utils.py | Python | mit | 1,385 | [
"pymatgen"
] | 203f5d13013a6e80207bf109fd317d480422412e028514a14a4aa479ba905d7b |
# Example of option baskets
# Distributed under BSD License
from enthought.mayavi.scripts import mayavi2
from enthought.tvtk.tools import mlab
from plotspace import PlotSpace
mayavi2.standalone(globals())
import eurooption
import basketoption
import scipy
import numpy
import threading
spot = scipy.arange(10.0, 100.0... | fabrice-lecuyer/QuantLib-SWIG | Python/examples/visualization/option.plotspace.py | Python | bsd-3-clause | 1,055 | [
"Mayavi"
] | e59f641774693d03216bfe81bd857484c2cca88361df67fdbf41718007242c87 |
# -*- coding: utf-8 -*-
"""
Kay framework.
:Copyright: (c) 2009 Accense Technology, Inc.
Takashi Matsuo <tmatsuo@candit.jp>,
Ian Lewis <IanMLewis@gmail.com>
All rights reserved.
:license: BSD, see LICENSE for more details.
"""
import os
import sys
import... | gmist/kay-ru | kay/__init__.py | Python | bsd-3-clause | 7,598 | [
"VisIt"
] | 09a140597de32e210bd6090b6c376049738cbd78f3bc4c0ac5d00ae885e652be |
#!/usr/bin/env python
# -*- coding: iso-8859-1 -*-
###########################################################################
# #
# ESPResSo++ Benchmark Python script for a polymer melt #
# ... | junghans/espressopp | bench/polymer_melt/espressopp/espressopp_polymer_melt.py | Python | gpl-3.0 | 5,235 | [
"ESPResSo",
"Gromacs",
"LAMMPS"
] | 8a49117e04f78159e4bf492a91fd4d2eedea59b207a85d82e6293671b97e22cd |
'''
Individual stages of the pipeline implemented as functions from
input files to output files.
The run_stage function knows everything about submitting jobs and, given
the state parameter, has full access to the state of the pipeline, such
as config, options, DRMAA and the logger.
'''
from utils import safe_make_di... | khalidm/thepipeline | src/stages.py | Python | bsd-3-clause | 19,586 | [
"BWA"
] | bdc1e4f1fd9ee46af7d13e2d25cac2222caa5f6e8f6b96e5ce2971e11f9ea9cc |
import re
import copy
import numpy
import math
import os
aaCode = {
'ALA' : 'A',
'ARG' : 'R',
'ASN' : 'N',
'ASP' : 'D',
'GLU' : 'E',
'GLN' : 'Q',
'GLY' : 'G',
'HIS' : 'H',
'CYS' : 'C',
'LYS' : 'K',
'MET' : 'M',
'LEU' : 'L',
'ILE' : 'I',
'MET' : 'M',
'PRO' : 'P',
'SER' : 'S',
'THR' : 'T',
'TRP' : 'W',... | glaunay/pyproteinsExt | src/pyproteinsExt/structure/coordinates.py | Python | gpl-3.0 | 15,192 | [
"PyMOL"
] | a326f4b81d439caf71cf43f05bf580667ef7c36df720ca54260926f0c7c40f8c |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | szha/mxnet | tests/python/unittest/test_gluon_probability_v2.py | Python | apache-2.0 | 93,370 | [
"Gaussian"
] | 4be41f2a7d492dc09fb7689989d433917a9f107465dd4b3bcc16e0fe4a714854 |
# Copyright 2020 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google-research/sound-separation | models/dcase2020_fuss_baseline/train/network_config.py | Python | apache-2.0 | 10,682 | [
"Brian"
] | 82c4be2f49b2ce2789f0ec75584f937545815b0be42851b1bbaa117ff3a65c78 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | amjames/psi4 | psi4/driver/p4util/optproc.py | Python | lgpl-3.0 | 4,939 | [
"Psi4"
] | 5f835fa83c614343f51ca0c8361e73415e1db3fe32dcd8a75ed8828be4ba9e4d |
from __future__ import division
import sys
assert sys.version_info[0:2] >= (2, 6)
import ast
class imported_name(object):
__slots__ = ('name', 'lineno')
def __init__(self, name, lineno):
self.name = tuple(name.split('.'))
self.lineno = lineno
def __eq__(self, other):
return (self.name == other.na... | hickerson/bbn | fable/fable_sources/libtbx/python_code_parsing.py | Python | mit | 7,002 | [
"VisIt"
] | 29043d331c801ff942b43bcbb065f3db004512d8fbb17dfcd6f36b26cc430957 |
#!usr/bin/python
# Copyright 2016, Rohan Dandage <rraadd_8@hotmail.com,rohan@igib.in>
# This program is distributed under General Public License v. 3.
"""
================================
``get_protein_features``
================================
"""
from os.path import exists,abspath,dirname,basename,splitext
from ... | rraadd88/dms2dfe | dms2dfe/lib/get_protein_features.py | Python | gpl-3.0 | 35,124 | [
"BLAST",
"pysam"
] | 3024985dd94ae8d719d865cf00fc385175ebf360419446ca3a8810920db43917 |
__author__ = "Sunil Kumar (kumar.sunil.p@gmail.com)"
__copyright__ = "Copyright 2014, Washington University in St. Louis"
__credits__ = ["Sunil Kumar", "Steve Pieper", "Dan Marcus"]
__license__ = "XNAT Software License Agreement " + \
"(see: http://xnat.org/about/license.php)"
__version__ = "2.1.1"
__main... | MokaCreativeLLC/XNATSlicer | XNATSlicer/XnatSlicerLib/io/Workflow_Save.py | Python | bsd-3-clause | 6,288 | [
"VTK"
] | db3f77ab7a88d1a8ee70ee725b6ce215f25acc99215660ae75f71d9fa66e8b1e |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This class implements smart io classes that performs intelligent io based on
file extensions.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email_... | rousseab/pymatgen | pymatgen/io/smart.py | Python | mit | 6,487 | [
"Gaussian",
"VASP",
"pymatgen"
] | 06183248490d18ca08605fb9adcadc08f768b9365e49aa66d0ae7c17168b029f |
#
# Copyright (c) 2010-2014, MIT Probabilistic Computing Project
#
# Lead Developers: Jay Baxter and Dan Lovell
# Authors: Jay Baxter, Dan Lovell, Baxter Eaves, Vikash Mansinghka
# Research Leads: Vikash Mansinghka, Patrick Shafto
#
# Licensed under the Apache License, Version 2.0 (the "License");
#... | JDReutt/BayesDB | bayesdb/engine.py | Python | apache-2.0 | 91,540 | [
"VisIt"
] | 3469a11501cb61bc1ac407acc7cd745eedab7f4c358b2da5f4258cb6542ea87a |
# Converts all the TOPO precursor files to NetCDF for easy perusal
#
| citibeth/twoway | topo/convert_input_files.py | Python | gpl-3.0 | 69 | [
"NetCDF"
] | e7f8a45d16ca2f7a35c24b0c644567375d820b31b706d066b644cfa008668cd8 |
"""
This file contains view functions for wrapping the django-wiki.
"""
import logging
import re
import cgi
from django.conf import settings
from django.contrib.sites.models import Site
from django.core.exceptions import ImproperlyConfigured
from django.shortcuts import redirect
from django.utils.translation import ug... | zhenzhai/edx-platform | lms/djangoapps/course_wiki/views.py | Python | agpl-3.0 | 4,924 | [
"VisIt"
] | f47020ec3c2fe8702eb388c18e7b61dffc55dbf192776105e548c0e48615e948 |
# This file is part of Androguard.
#
# Copyright (c) 2012 Geoffroy Gueguen <geoffroy.gueguen@gmail.com>
# 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://... | shuxin/androguard | androguard/decompiler/dad/basic_blocks.py | Python | apache-2.0 | 11,271 | [
"VisIt"
] | 96d4529bf3ed709d4971b8c9e3e0c9364b7a53b27f9270324698bf9059ddb585 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import unicode_literals, division, print_function
"""
Error handlers for errors originating from the Submission systems.
"""
__author__ = "Michiel van Setten"
__copyright__ = " "
__version__ =... | migueldiascosta/pymatgen | pymatgen/io/abinit/scheduler_error_handlers.py | Python | mit | 3,465 | [
"ABINIT",
"pymatgen"
] | 4cc9390ac87750f694eea79d2c0390464802754d675850d14765d666e96b763f |
# sklearnTrainer
import numpy
import numpy as np
import copy
from toolkitJ import cell2dmatlab_jsp
import matplotlib as mpl
from matplotlib.font_manager import FontProperties
zhfont = FontProperties(fname="/usr/share/fonts/cjkuni-ukai/ukai.ttc") # 图片显示中文字体
mpl.use('Agg')
import pprint
from sklearn.ex... | tabhitmy/MLTF | WORKFLOW/code/python_code/sklearnTrainer.py | Python | mit | 12,746 | [
"Gaussian"
] | 65dfac4d9f522d7f113a0ca7b8185ac7ee01d4d62937cd362a346a4f1c7b9e1b |
import collections
import copy
import heapq
import traceback
import warnings
import weakref
import numpy
import six
import chainer
from chainer import cuda
from chainer import initializers
from chainer.initializers import constant
from chainer import utils
from chainer.utils import argument
def _check_grad_type(fun... | ysekky/chainer | chainer/variable.py | Python | mit | 34,072 | [
"VisIt"
] | 288cc4c20525942101aeeae437f4b250f94425cbdcecd68f47f6402e637fbcad |
#!/usr/bin/python
# -*- encoding: utf-8 -*-
# region gplv3preamble
# The Medical Simulation Markup Language (MSML) - Simplifying the biomechanical modeling workflow
#
# MSML has been developed in the framework of 'SFB TRR 125 Cognition-Guided Surgery'
#
# If you use this software in academic work, please cite the paper... | CognitionGuidedSurgery/msml | examples/ColorExample/color-example.py | Python | gpl-3.0 | 2,520 | [
"ParaView",
"VTK"
] | 32ac1231bb3e73fa69c1064169bbde41fdd074fde2af7acd2f997e32dd8a1d18 |
import pysal
import os.path
import struct
import pysal.core.FileIO as FileIO
from pysal.weights import W
from warnings import warn
__author__ = "Myunghwa Hwang <mhwang4@gmail.com>"
__all__ = ["Wk1IO"]
class Wk1IO(FileIO.FileIO):
"""
Opens, reads, and writes weights file objects in Lotus Wk1 format.
Lotu... | AlanZatarain/pysal | pysal/core/IOHandlers/wk1.py | Python | bsd-3-clause | 11,380 | [
"Brian"
] | c5fd2aa3247a44bbdd067fce7ef0881a923fa1c9a5b86bcb3a0db494cd54c95b |
#!/usr/bin/python
import sys
import time
import threading
import os
BOREALISPATH = os.environ['BOREALISPATH']
sys.path.append(BOREALISPATH)
sys.path.append(os.environ["BOREALISPATH"] + '/build/release/utils/protobuf')
from utils.zmq_borealis_helpers import socket_operations as so
from utils.experiment_options.experi... | SuperDARNCanada/placeholderOS | tools/simulators/radar_control_input_sim/radar_control_input_sim.py | Python | gpl-3.0 | 4,040 | [
"Brian"
] | 8bb9bd59e594a2a8b37f636a6705b4ab9e9aaff985d60accf18a2f197f4178a6 |
# Copyright 2007-2022 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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 ve... | jat255/hyperspy | hyperspy/tests/component/test_component_set_parameters.py | Python | gpl-3.0 | 1,914 | [
"Gaussian"
] | ec4c8b2006d32722b87db48054689422d64b3dc64a8719e71902aab283cd4aef |
import time
import json
import datetime
from firefly.common import pixlib
from firefly.objects import has_right
from firefly.widgets import ToolBarStretcher, ChannelDisplay
from firefly.qt import (
Qt,
QAction,
QToolBar,
QDialog,
QCalendarWidget,
QVBoxLayout,
QDate,
QToolButton,
QIc... | immstudios/firefly | firefly/modules/rundown_utils.py | Python | gpl-3.0 | 5,396 | [
"Firefly"
] | 74784705a1510d9ca17691e396ab04ae5fcce6dbcfdd38d63ffcadceeb11b40e |
# 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
# version.
#
# This program is distributed in the hope that it will be useful, but ... | shaleh/clonedigger | clonedigger/logilab/common/visitor.py | Python | gpl-3.0 | 3,686 | [
"VisIt"
] | fe28e3d7976b32657735dab56cfeb31964ffa2ffb8fd557eb41b5ee721930f2d |
from tractconverter.utils import convert
from tractconverter.utils import merge
from tractconverter.utils import is_supported
from tractconverter.utils import detect_format
from tractconverter.utils import FORMATS
from tractconverter.utils import EXT_ANAT
from tractconverter.formats.tck import TCK
from tractconverter.... | MarcCote/tractconverter | tractconverter/__init__.py | Python | bsd-3-clause | 429 | [
"VTK"
] | d603e710dedc9b6ad4cd52c3e22555a41f6af541344799d1bd9d6bfb7f004a6b |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes to perform fitting of structures.
"""
from __future__ import division, unicode_literals
import six
from six.moves import filter
from six.moves import zip
import numpy as np
i... | xhqu1981/pymatgen | pymatgen/analysis/structure_matcher.py | Python | mit | 42,586 | [
"pymatgen"
] | 0cca8eb99386fb2b129aabe2eac58802097c19733f0a8c29216b1e0c6325c624 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import random
import unittest
from collections import Counter
import numpy as np
from pymatgen.analysis.defects.utils import (
ChargeDensityAnalyzer,
ChargeInsertionAnalyzer,
QModel,
StructureMotif... | vorwerkc/pymatgen | pymatgen/analysis/defects/tests/test_utils.py | Python | mit | 15,764 | [
"VASP",
"pymatgen"
] | 1d28bb27c41e7d43ecf30963cb8c130c1ff605fde940f3835b192e25ee3ec6f7 |
import os
import re
import copy
import collections
import logging
import MooseDocs
import collections
import subprocess
import yaml
log = logging.getLogger(__name__)
class PagesHelper(object):
"""
A helper class for checking if a markdown file is include in the 'pages.yml' file.
"""
def __init__(self,... | katyhuff/moose | python/MooseDocs/MooseApplicationSyntax.py | Python | lgpl-2.1 | 13,523 | [
"MOOSE"
] | e64222f445e08d12e3c6ca7496807be152707ef1b76b3c0ab224e1ac4602e84f |
# -*- coding: utf-8 -*-
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import absolute_import
from __future__ import division
from math import ceil
from six.moves import zip_longest
import logging
from osgeo import osr
import netCDF4
import numpy as np
from flooding_li... | lizardsystem/flooding | flooding_lib/tools/threeditool/quads.py | Python | gpl-3.0 | 9,210 | [
"NetCDF"
] | 9fa97c03a6428bebc13dd860991f87365e583ba47bcb8dc1467b5b52ef54e937 |
#Example of python/Visit plotting for Gamera
#Assuming visGam is in python path
#This shows field loop advection in a warped grid (warpFL.xml)
import sys
import os
import numpy as np
from visit import *
from visit_utils import *
from visit_utils.common import lsearch #lsearch(dir(),"blah")
import visGam as vg
import p... | ksorat/Gamera | viz/vidEx.py | Python | gpl-3.0 | 2,014 | [
"VisIt"
] | c6197ccc5c74daa42fe27d04212e6f3cd4605baa4184e335f080646fd9daf38d |
##
# Copyright 2013 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (http://w... | ULHPC/modules | easybuild/easybuild-easyblocks/easybuild/easyblocks/e/esmf.py | Python | mit | 4,181 | [
"NetCDF"
] | 26d8cf9a69808893e8b2320f0da7535aecb002c596304c731f58cb3053bf8215 |
# -*- coding: utf-8 -*-
"""
Created on Thu Feb 11 16:45:59 2016
Functions for mom bud analysis in module vtk_mom_bud_analyse.py
@author: sweel
"""
from collections import defaultdict
import matplotlib.pyplot as plt
from mayavi import mlab
import pandas as pd
plt.rcParams['font.family'] = 'DejaVu Sans'
# pylint: disabl... | moosekaka/sweepython | mombud/vtk_viz/vtk_mbfuncs.py | Python | mit | 2,958 | [
"Mayavi"
] | a5f7b97631b8e1d0c96a73e8c005a9a151615dd78fd4367145f8251ca7cee0ad |
# -*- coding: utf-8 -*-
"""
PyBioMed
========
PyBioMed is a feature-rich packages used for the characterization of various complex biological molecules and interaction samples, such as chemicals, proteins, DNA, and their interactions. In order to be convenient to users, PyBioMed provides the module to get molecule st... | gadsbyfly/PyBioMed | PyBioMed/__init__.py | Python | bsd-3-clause | 1,232 | [
"Discovery Studio",
"MOE",
"RDKit"
] | e2b42cc39c6e05d9bc79484bb35a38c1ea311b22069873c721036cbbbebff187 |
""" X509Certificate is a class for managing X509 certificates
Proxy RFC: https://tools.ietf.org/html/rfc38200
X509RFC: https://tools.ietf.org/html/rfc5280
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import datetime
import os
im... | ic-hep/DIRAC | src/DIRAC/Core/Security/m2crypto/X509Certificate.py | Python | gpl-3.0 | 15,782 | [
"DIRAC"
] | 7432e66f0c40a9a2edb900aaf3b64353877605b5c9df803ad8173a519a61404b |
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
from lettuce import world, step
from lettuce.django import django_url
from django.conf import settings
import requests
import string
import random
import os
from django.contrib.auth.models import User
from student.models import CourseEnrollment... | ahmadiga/min_edx | cms/djangoapps/contentstore/features/upload.py | Python | agpl-3.0 | 7,493 | [
"VisIt"
] | e2a8395ca2a8a23dd0076fa28ee4536faa7987fb12ccfa1b1db2764ab0abe1e3 |
# -*- encoding: utf-8 -*-
"""
Flask-Espresso
==============
Adds Coffeescript [0] support to Flask [1] applications.
Flask-Espresso will compile on the fly your coffee-scripts in the template
directory of your application. To avoid performance issues, a cache mechanism
retrieves the scripts already compiled.
Instal... | morgan-del/flask-espresso | setup.py | Python | bsd-2-clause | 2,079 | [
"ESPResSo"
] | f3ad79a2586174c45a9b0f5773c61a09ada9ef6edfc9b78ce8cd9e01c8406658 |
#!/usr/bin/env python
import os.path
from django.conf import settings
from django.test import TransactionTestCase
from django.test.client import Client
from django.utils import simplejson as json
from panda.models import DataUpload
from panda.tests import utils
class TestAPIDataUpload(TransactionTestCase):
fixt... | PalmBeachPost/panda | panda/tests/test_api_data_upload.py | Python | mit | 4,941 | [
"Brian"
] | 9d8260f6f2d9eb288e03350d1b1fa1ceaefcb3944f1d6f380c9d41a39bb921fa |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=80 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# -------------------------------------------------------... | marmyshev/transitions | openlp/plugins/songs/lib/test/test_import_file.py | Python | gpl-2.0 | 2,701 | [
"Brian"
] | 5ee634101c42a3d588e2e359cfaa3d3e79d2c004ebacb7039f6e518d3e43f8fc |
from . import tempdir as td
import os
import pybol
import gromacs
import mdpow
from mdpow.equil import Simulation
from mdpow.run import fep_simulation
from mdpow.config import get_configuration
from . import RESOURCES
class TestFEPScript(object):
def setup(self):
self.tmpdir = td.TempDir()
self... | Becksteinlab/MDPOW | mdpow/tests/test_fep_script.py | Python | gpl-3.0 | 2,145 | [
"Gromacs"
] | b7ecfe339709b154bc613c839f9fe02eb285753753c78a3053c96ea5580605ba |
#!/usr/bin/env python
"""
WalkCow, VTK Textbook figure 3-33b.
Note: Make sure WalkCow.py is in the same directory as this program.
"""
import WalkCow
def main():
file_name, figure = WalkCow.get_program_parameters()
figure = 2
WalkCow.walk_cow(file_name, figure)
if __name__ == '__main__':
main()
| lorensen/VTKExamples | src/Python/Rendering/WalkCowB.py | Python | apache-2.0 | 319 | [
"VTK"
] | 450c4ae5e14e99f375f5f1d84eaa5c105cd1b8dc1aaf78f3d2f9d2710ca9d43c |
"""
plink2 Galaxy Wrapper
Mark Einon <mark.einon@gmail.com>
based on plink.py version 0.1 (andrea.pinna@crs4.it)
"""
import optparse
import os
import shutil
import subprocess
import sys
def filter_outputs(prefix, extension, newname=''):
cwd = os.getcwd()
outdir = 'outputs%s' % extension
os.mkdir(outdi... | einon/galaxy-tools | plink2/plink2.py | Python | gpl-3.0 | 5,340 | [
"Galaxy"
] | b76cafd5a8a0d53bb4b3114ba358315bb6aa61497dab0bb87b91eb375b72308c |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
import datetime
from django.conf import settings
from django.http import HttpResponse
from django.test import TestCase
from mock import patch
from zerver.lib.test_helpers import MockLDAP
from confirmation.models import Confirmation
from zilencer.models i... | sonali0901/zulip | zerver/tests/test_signup.py | Python | apache-2.0 | 52,046 | [
"VisIt"
] | 7db6f0873caae49748aaffb30d13522a99380150a5f3ef137c58751792ca61d6 |
# $Id: BMPRDR.py 1853 2006-02-01 17:16:28Z cpbotha $
from module_base import ModuleBase
from module_mixins import ScriptedConfigModuleMixin
import module_utils
import vtk
import wx
class BMPReader(ScriptedConfigModuleMixin, ModuleBase):
def __init__(self, module_manager):
ModuleBase.__init__(self, mo... | nagyistoce/devide | modules/readers/BMPReader.py | Python | bsd-3-clause | 3,607 | [
"VTK"
] | c747d498abad522f6a17bc225cbd936a617ab36b05a5a46effce0f6b7a39b0be |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | pierrelapointe/scancode-toolkit | src/cluecode/copyrights.py | Python | apache-2.0 | 32,051 | [
"VisIt"
] | 6207a55f7bc3290d4022df4a0cfe40ac46c290dc9dee643080a75e9c95d39110 |
# (C) British Crown Copyright 2014 - 2015, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | Jozhogg/iris | lib/iris/tests/unit/fileformats/pyke_rules/compiled_krb/fc_rules_cf_fc/test_build_dimension_coordinate.py | Python | lgpl-3.0 | 15,401 | [
"NetCDF"
] | 5ca722294094aed754a01440e0dd77bb9464150eb70d9181a84f171ea47db733 |
import pandas as pd
from skgstat.data import _loader
from skgstat.data._loader import field_names, sample_to_df
# define all names
names = field_names()
origins = dict(
pancake="""Image of a pancake with apparent spatial structure.
Copyright Mirko Mälicke, 2020. If you use this data,
cite SciKit-GStat: h... | mmaelicke/scikit-gstat | skgstat/data/__init__.py | Python | mit | 9,465 | [
"Gaussian"
] | 377bdafe0a0292e822bcb1352794fbfe52aa2e8c815878f516b67b36a07f37db |
"""A .. collapse:: directive for sphinx-bootstrap-theme."""
import os.path as op
from docutils import nodes
from docutils.parsers.rst.directives import flag, class_option
from docutils.parsers.rst.roles import set_classes
from docutils.statemachine import StringList
from sphinx.locale import _
from sphinx.util.docuti... | bloyl/mne-python | doc/sphinxext/sphinx_bootstrap_divs/__init__.py | Python | bsd-3-clause | 6,103 | [
"VisIt"
] | 3fadcc730917ef6cf3fe95ae6cf96ef9e096d2c8cdd623a1ec8c6d26c78994f7 |
#!/usr/bin/env python
'''
Copyright 2017 Matt Settles
Created June 8, 2017
bwa mem -C option concatenats the fasta/fastq
CTACATTGTCAAGGGT:E00558:34:HGCJ3ALXX:1:1101:2108:1731 99 000000F 922571 60 127M = 922961 517 ACTCGGGGAGGTGTTAGCTGCTGCCTCACACATTGGGTTTATAGGCTGAATCTTGTTCTCTTTAGGCTTCCAGAGTTT... | ucdavis-bioinformatics/proc10xG | samConcat2Tag.py | Python | apache-2.0 | 3,360 | [
"BWA"
] | ac9bbe39d3be138a2888b0b8a5273a931b5ded7dfd69a91b8ca3384f3f2fe6d9 |
from datetime import tzinfo, timedelta, datetime, timezone
ZERO = timedelta(0)
HOUR = timedelta(hours=1)
SECOND = timedelta(seconds=1)
# A class capturing the platform's idea of local time.
# (May result in wrong values on historical times in
# timezones where UTC offset and/or the DST rules had
# changed in the pa... | DeanAaron/Python3 | python-3.8.0a0-docs-html-en/_downloads/tzinfo_examples.py | Python | gpl-3.0 | 5,870 | [
"VisIt"
] | 6c4ba035b0ed6bd11ea370380a8c6b57b917df4be903e1bd4292358e11fe483f |
## INFO ########################################################################
## ##
## plastey ##
## ======= ... | kitchenbudapest/vr | hud.py | Python | gpl-3.0 | 4,413 | [
"VisIt"
] | e967c748a0685a09b1a427a5cf1247d9896b26b0b45477ce45a20b4aa32c5548 |
# CREATED:2013-08-19 16:12:01 by Brian McFee <brm2132@columbia.edu>
#
# Ordinal LDA
import itertools
import numpy as np
import scipy.linalg
from sklearn.base import BaseEstimator, TransformerMixin
class OLDA(BaseEstimator, TransformerMixin):
def __init__(self, sigma=1e-4):
'''Ordinal linear discriminant ... | urinieto/msaf | msaf/algorithms/olda/OLDA.py | Python | mit | 4,026 | [
"Brian"
] | cade658c00fd8317974ac32110f93d29300b432466318f0d0cd534b3d0d4dbca |
# Generated from /cci_src/imap2017/src/imap-search-parser/python-emitter/imap2017search.g4 by ANTLR 4.6
from antlr4 import *
if __name__ is not None and "." in __name__:
from .imap2017searchParser import imap2017searchParser
else:
from imap2017searchParser import imap2017searchParser
# This class defines a com... | chromatic-universe/imap2017 | src/imap-search-parser/python-emitter/gen/imap2017searchVisitor.py | Python | mit | 15,026 | [
"VisIt"
] | 7ada826d8912c3e5870aba02bc88489fa6e9856c80d6640ba8ab618a878044f3 |
# Version: 0.15
"""
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, and pypy
* [![Latest Version]
(https://pypip.in/version/versioneer/badge.svg?style=flat)
](htt... | ppinard/matplotlib-colorbar | versioneer.py | Python | bsd-2-clause | 62,522 | [
"Brian"
] | 524d579b94401b75c319da722ff552a0ec2adcb34e07b0abd0d7c85b0fb0f976 |
#!/usr/bin/env python3
"""
Gather different information from a Galaxy server (by default https://usegalaxy.org)
and EDAM ontology (by default from http://edamontology.org/EDAM.owl)
"""
# Import ------------------------------
# General libraries
import os
import json
import logging
# External libraries
import requ... | khillion/ToolDog | tooldog/annotate/edam_to_galaxy.py | Python | mit | 14,711 | [
"Galaxy"
] | 98e4f55f18fd62ea20b4668200938cea0460f94a23175d11009335bc4ff3d39b |
#
# @file TestL3Model.py
# @brief L3 Model unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting the file located at
# ... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestL3Model.py | Python | bsd-3-clause | 8,969 | [
"VisIt"
] | 29766f644b252196b41ef6ad2ae49b2cc56c9f3051b282ed168ea39c45a7a3b5 |
from unittest import TestCase
from six import assertRaisesRegex
import warnings
from dark.genbank import GenomeRanges
class TestErrors(TestCase):
"""
Test incorrect ways of instantitating the GenomeRanges class.
"""
def testEmptyString(self):
"""
The GenomeRanges class must raise a Va... | terrycojones/dark-matter | test/test_genbank.py | Python | mit | 18,296 | [
"Biopython"
] | f42d88bfbac7a49f0299107c2c51140d31abea331a9effbdae4bec6af1d2f512 |
"""An interface for publishing rich data to frontends.
There are two components of the display system:
* Display formatters, which take a Python object and compute the
representation of the object in various formats (text, HTML, SVg, etc.).
* The display publisher that is used to send the representation data to the... | cloud9ers/gurumate | environment/lib/python2.7/site-packages/IPython/core/displaypub.py | Python | lgpl-3.0 | 9,739 | [
"Brian"
] | 8a1575ad9c352265a06544a03833b0f0fd707be84615c1a77c99c3283a90141f |
#!/usr/bin/env python
import os, sys, re
import pysam
import threading
usage = "\n\n\tusage: " + sys.argv[0] + " alignments.bam left.fq right.fq\n\n"
if len(sys.argv) < 4:
print >>sys.stderr, usage
sys.exit(1)
alignments_bam = sys.argv[1]
left_fq_filename = sys.argv[2]
right_fq_filename = sys.argv[3]
MIN_... | DISCAFUSE/DISCAFUSE | util/retrieve_discordant_and_unmapped_reads.py | Python | bsd-3-clause | 2,824 | [
"pysam"
] | 00ed85ad554c7861f56d86bcea905f71c9aeea5a6f022e16f6ac04825c3279c7 |
# ##### BEGIN GPL LICENSE BLOCK #####
#
# 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 version.
#
# This program is distrib... | michielkleinnijenhuis/NeuroBlender | examples/example1/example1.py | Python | gpl-3.0 | 18,484 | [
"VTK"
] | da21647adad3428b0df8182bef7be107f6605e0565f01c9fab612e52883aaefb |
# Pizza.py toolkit, www.cs.sandia.gov/~sjplimp/pizza.html
# Steve Plimpton, sjplimp@sandia.gov, Sandia National Laboratories
#
# Copyright (2005) Sandia Corporation. Under the terms of Contract
# DE-AC04-94AL85000 with Sandia Corporation, the U.S. Government retains
# certain rights in this software. This software is... | sleepingZ/KerosPore | tools/vmd.py | Python | gpl-3.0 | 8,763 | [
"VMD"
] | 4d0b963f6331cd454b94d29c66af5bbdc8efc70232e3810d54c92f1d942f3847 |
import warnings
from pandas import DateOffset, DatetimeIndex, Series, Timestamp
from pandas.compat import add_metaclass
from datetime import datetime, timedelta
from dateutil.relativedelta import MO, TU, WE, TH, FR, SA, SU
from pandas.tseries.offsets import Easter, Day
import numpy as np
def next_monday(dt):
"""... | Vvucinic/Wander | venv_2_7/lib/python2.7/site-packages/pandas/tseries/holiday.py | Python | artistic-2.0 | 15,920 | [
"COLUMBUS"
] | ef38d37ed572f5409e6e68202f2456e47d86b367afd0aa04f60c5cf548f7f743 |
import unittest
from mock import Mock
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities.ObjectLoader import ObjectLoader
from DIRAC.Core.DISET.RequestHandler import RequestHandler
class ObjectLoaderMainSuccessScenario( unittest.TestCase ):
def setUp( self ):
self.ol = ObjectLoader()
def __check( sel... | avedaee/DIRAC | Core/Utilities/test/ObjectLoaderTests.py | Python | gpl-3.0 | 971 | [
"DIRAC"
] | 1ca5d934f2da22ce33df1d8329991329feb88e2855949fc37e4e0aba4094c4b6 |
# coding: utf-8
from __future__ import unicode_literals
import itertools
import json
import os.path
import random
import re
import traceback
from .common import InfoExtractor, SearchInfoExtractor
from ..compat import (
compat_chr,
compat_HTTPError,
compat_parse_qs,
compat_str,
compat_urllib_parse... | yasoob/youtube-dl-GUI | youtube_dl/extractor/youtube.py | Python | mit | 141,910 | [
"ADF"
] | 651ba47e7a5cccb1d2b9a39b9ec0ddea9a339c827692ec925b69e4058245a4fe |
# 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)
import os
from spack import *
class Parflow(CMakePackage):
"""ParFlow is an open-source parallel watershed simulato... | LLNL/spack | var/spack/repos/builtin/packages/parflow/package.py | Python | lgpl-2.1 | 3,199 | [
"NetCDF"
] | e7b64f4a69413d302f6f3c4451b4a141e53d80fac41992854a122581ff7088b9 |
"""Simple XML-RPC Server.
This module can be used to create simple XML-RPC servers
by creating a server and either installing functions, a
class instance, or by extending the SimpleXMLRPCServer
class.
It can also be used to handle XML-RPC requests in a CGI
environment using CGIXMLRPCRequestHandler.
A list of possibl... | trivoldus28/pulsarch-verilog | tools/local/bas-release/bas,3.9/lib/python/lib/python2.3/SimpleXMLRPCServer.py | Python | gpl-2.0 | 17,561 | [
"Brian"
] | 17ac13b3f0e426b485400e0568b811fc1f5c2f0d558bf1818231d2f73c14e9d4 |
"""
Copyright (c) 2016 Jet Propulsion Laboratory,
California Institute of Technology. All rights reserved
"""
import ConfigParser
import importlib
import json
import logging
import sys, os
import traceback
from multiprocessing.pool import ThreadPool
import matplotlib
import pkg_resources
import tornado.web
from torna... | dataplumber/nexus | analysis/webservice/webapp.py | Python | apache-2.0 | 9,031 | [
"NetCDF"
] | ff664fadd403f417e6db9ece759cd915d2e5b75d626a37ea5f7d6275a7a373ae |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# base - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the ... | heromod/migrid | mig/shared/distos/base.py | Python | gpl-2.0 | 14,183 | [
"Brian"
] | 70de15833281dd1185de484df4385da11d2e38ff88dcb4db8071a872b05e2732 |
'''
Created on 2013-05-02
@author: brian
'''
import pygame
from pygame.locals import *
from src.util import Cardinal
class Build:
def __init__(self, player):
self.player = player
self.direction = None
self.finished = False
self.player.log.append('Build... (Choose a block)')
self.choices = {}
bag = pla... | Greymerk/python-rpg | src/actions/build.py | Python | gpl-3.0 | 1,923 | [
"Brian"
] | 6991c1317b05ab357e03c64379c110d4d3f719dd58038d58f87aa40c6108cd4a |
'''
Downloads the actual gm results most recently generated by the Skia buildbots,
and adds any new ones to SVN control.
Launch with --help to see more information.
Copyright 2011 Google Inc.
Use of this source code is governed by a BSD-style license that can be
found in the LICENSE file.
'''
# common Python modul... | Gateworks/skia | tools/download_baselines.py | Python | bsd-3-clause | 9,990 | [
"Galaxy"
] | ed20473c76ead594f907fd86c4260ad6426ec7dab59d5d9cad3d8dad650b9c22 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.