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"""
This is a program use for scale VCF file into small ones by
custom parameter. And compress all the sub-file by bgzip and
build the tabix index.
Copyright (c) Shujia Huang
Date: 2015-08-11
"""
import sys
import os
import re
import optparse
import string
import time
from subprocess import Popen, PIPE
import pysam ... | ShujiaHuang/AsmVar2 | scripts/scale.py | Python | mit | 10,816 | [
"pysam"
] | d314cfdd948f09fa12afc4e746f785761a262be62d19e9869605fc40a7014fe3 |
# -*- coding: utf-8 -*-
"""
PyOpenWorm
==========
OpenWorm Unified Data Abstract Layer.
Classes
-------
.. autoclass:: Network
:members:
.. autoclass:: Neuron
:members:
.. autoclass:: Worm
:members:
.. autoclass:: Muscle
:members:
"""
__version__ = '0.0.1'
__author__ = 'Stephen Larson'
from .configure... | mwatts15/PyOpenWorm | PyOpenWorm/__init__.py | Python | mit | 764 | [
"NEURON"
] | 21e723364a1cfd4eed6f5328d791a4a8ec600d45fd8576b2ba35d416aef072ce |
mnemonics = {
"NOP": b'\x00\x00',
"STA": b'\x10\x00',
"LDA": b'\x20\x00',
"ADD": b'\x30\x00',
"OR": b'\x40\x00',
"AND": b'\x50\x00',
"NOT": b'\x60\x00',
"JMP": b'\x80\x00',
"JN": b'\x90\x00',
"JZ": b'\xA0\x00',
"HLT": b'\xF0\x00'
}
import collections
import re
import type... | dsvictor94/neander-compiler | compiler.py | Python | mit | 10,505 | [
"VisIt"
] | b6d4d73f6d3a6c5ddcb576465bec57cd50ad805d44070e1e14f8974efa5a12ef |
"""
Window functions (:mod:`scipy.signal.windows`)
==============================================
The suite of window functions for filtering and spectral estimation.
.. currentmodule:: scipy.signal.windows
.. autosummary::
:toctree: generated/
get_window -- Return a window of a given length and type.
... | grlee77/scipy | scipy/signal/windows/__init__.py | Python | bsd-3-clause | 1,771 | [
"Gaussian"
] | fa9c9b996a9507261a435a3b3d8694b8cd079ba655c9fb065c46c05e059cc2de |
from redux.ast import ASTNode
import logging
class Visitor(object):
"Implements the extrinsic Visitor pattern."
def __init__(self):
super(Visitor, self).__init__()
self.depth = 0
def log(self, fmt, *args, **kwargs):
logging.getLogger(type(self).__name__).debug("%s%d: " + fmt, " ... | Muon/redux | redux/visitor.py | Python | mit | 2,625 | [
"VisIt"
] | 2966b0045e52e30c77edef5c986d7cbb379b61f5f54b866466ede539787c4dac |
#!/usr/bin/env python3
##############################################################################
# Copyright (c) 2021: Leonardo Cardoso
# https://github.com/LeoFCardoso/pdf2pdfocr
##############################################################################
# OCR a PDF and add a text "layer" in the original file ... | LeoFCardoso/pdf2pdfocr | pdf2pdfocr.py | Python | apache-2.0 | 73,585 | [
"Gaussian"
] | c26036c08232b2594b63afe97f74a5c133d53ffd32be83cf650b2375149eabd4 |
"""cursor_handler.py - Cursor handler."""
import gobject
import gtk
from mcomix import constants
class CursorHandler:
def __init__(self, window):
self._window = window
self._timer_id = None
self._auto_hide = False
self._current_cursor = constants.NORMAL_CURSOR
def set_cursor... | mxtthias/mcomix | mcomix/cursor_handler.py | Python | gpl-2.0 | 2,509 | [
"FLEUR"
] | b24cb22d078712f30b2fe4a6e756200f769833b4a9f468dcef2aa1e1ae83c34b |
#!/usr/bin/env python
from setuptools import setup, Extension
from Cython.Distutils import build_ext
from Cython.Build import cythonize
setup(
name='shand',
version='0.1',
description='A pipeline for investigating cospeciation in microbiomes',
scripts=['scripts/shand'],
url='http://github.com/rynec... | ryneches/Shand | setup.py | Python | bsd-3-clause | 717 | [
"scikit-bio"
] | 537a8375b935879d5164f21b03fbacef1f02a06ee5b1f02949070381c017f5eb |
"""
This is only meant to add docs to objects defined in C-extension modules.
The purpose is to allow easier editing of the docstrings without
requiring a re-compile.
NOTE: Many of the methods of ndarray have corresponding functions.
If you update these docstrings, please keep also the ones in
core/fromnum... | gfyoung/numpy | numpy/core/_add_newdocs.py | Python | bsd-3-clause | 211,533 | [
"Brian"
] | 692f32c18410287e1bf650a1424dca659c267a68d17972b95ea2a4b653f83b58 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import os
import re
import sys
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
def get_version(*file_paths):
"""Retrieves the version from djcloudbridge/__init__.py"""
filename = os.path.join(os.path.dirname(__file__... | CloudVE/djcloudbridge | setup.py | Python | mit | 3,003 | [
"Galaxy"
] | b15369ac6a40f763db755eb98474ebc3d099f265a4bae989edccd2696abef194 |
# Copyright 2018 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 applicab... | cshallue/models | research/deep_contextual_bandits/bandits/algorithms/bb_alpha_divergence_model.py | Python | apache-2.0 | 13,407 | [
"Gaussian"
] | 88ed77e34ea9e2c844dda9f4469e3f0d97024249a9e7f250ceb64009cbfa96b4 |
from __future__ import print_function
import numpy as np
import cv2
#import tensorflow as tf
import sys
sys.path.append('./agent')
sys.path.append('./deep_feedback_learning')
from agent.doom_simulator import DoomSimulator
#from agent.agent import Agent
from deep_feedback_learning import DeepFeedbackLearning
import thre... | nlholdem/icodoom | ICO1/run_agent.py | Python | gpl-3.0 | 19,933 | [
"NEURON"
] | fbdf068d35fd248c961b0bc8fd73e5beab49125cbf5304ff9b6a330088e5fd8c |
# $Id: dbexts.py,v 1.1 2005/10/05 20:19:27 eytanadar Exp $
"""
This script provides platform independence by wrapping Python
Database API 2.0 compatible drivers to allow seamless database
usage across implementations.
In order to use the C version, you need mxODBC and mxDateTime.
In order to use the Java vers... | carvalhomb/tsmells | guess/src/Lib/dbexts.py | Python | gpl-2.0 | 21,345 | [
"Brian"
] | 41973adf6984adb105971f50b02cd891497835267e01422ae1b16c360627b47e |
import glob, pyraf, time, numpy
from scipy import interpolate
from fitsfitter_MOD import *
from flux_level import *
from flux_level2 import *
from plotFLUX import *
#Retrieve dictionary
lib_path = os.path.abspath('/Users/npastorello/Desktop/Galaxies/General_studies/')
sys.path.append(lib_path)
from galaxyParametersDi... | pastorenick/SuperSKiMS_reduction | SKiMS_red__def__.py | Python | gpl-2.0 | 27,175 | [
"Galaxy"
] | c0ce686b879e10c9b317cef6f55a25a35f9323494c280e01ec40f8d8520201ea |
#
# 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 us... | iemejia/incubator-beam | sdks/python/apache_beam/runners/direct/consumer_tracking_pipeline_visitor_test.py | Python | apache-2.0 | 5,990 | [
"VisIt"
] | f41cfc5556e7a8b4dac848309669c01e90610373cd76d3d97868f517d9f01b65 |
# coding: utf-8
"""
Collection of low-level tools that faciliate the interface with resource managers.
The preferred way of importing this module is:
import qutils as qu
"""
from monty.string import is_string
from pymatgen.core.units import Time, Memory
import logging
logger = logging.getLogger(__name__)
def ... | dongsenfo/pymatgen | pymatgen/io/abinit/qutils.py | Python | mit | 3,697 | [
"pymatgen"
] | 867df861b5aac0704f6537483dfe2d944f78641d71dacff0d9076fb97853609e |
# coding=utf-8
# --------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See License.txt in the project root for license information.
# Code generated by Microsoft (R) AutoRest Code Generator.
# Changes may ... | Azure/azure-sdk-for-python | sdk/databoxedge/azure-mgmt-databoxedge/azure/mgmt/databoxedge/v2020_09_01/models/_models.py | Python | mit | 191,540 | [
"ASE"
] | 3a7bf745eebf0b32f19da55b24f3a83dd3872be3a10e101678df2dd6f1338234 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Generated from FHIR 4.0.0-a53ec6ee1b on 2019-05-07.
# 2019, SMART Health IT.
import os
import io
import unittest
import json
from . import encounter
from .fhirdate import FHIRDate
class EncounterTests(unittest.TestCase):
def instantiate_from(self, filename):
... | all-of-us/raw-data-repository | rdr_service/lib_fhir/fhirclient_4_0_0/models/encounter_tests.py | Python | bsd-3-clause | 31,172 | [
"VisIt"
] | 952e9cef1bd365ee3fb9f820b6b85d87050dba88a9e2b687b39d6305272f3a63 |
# -*- coding: utf-8 -*-
"""
Created on Tue Aug 25 13:08:19 2015
@author: jgimenez
"""
from PyQt4 import QtGui, QtCore
from postpro_ui import Ui_postproUI
from PyFoam.RunDictionary.ParsedParameterFile import ParsedParameterFile
from PyFoam.RunDictionary.BoundaryDict import BoundaryDict
import os
from matplotlib.figure... | jmarcelogimenez/petroSym | petroSym/postpro.py | Python | gpl-2.0 | 6,201 | [
"VTK"
] | 8fa22c48b8beaf6c07d6287efecef4e0dc759841af8c83a3ae68c5508e4ce81a |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the standard renderer, render window
# and interactor
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowIn... | hlzz/dotfiles | graphics/VTK-7.0.0/Rendering/Volume/Testing/Python/TestPTZSweep.py | Python | bsd-3-clause | 2,739 | [
"VTK"
] | de395fe76b4914c78775d89ad76de5585430045cb582d85a339f1e7493d99d0d |
"""
Implements a well defined versioning schema.
There are three class types - VersionToken, Version and VersionRange. A Version
is a set of zero or more VersionTokens, separate by '.'s or '-'s (eg "1.2-3").
A VersionToken is a string containing alphanumerics, and default implemenations
'NumericToken' and 'Alphanumeri... | ToonBoxEntertainment/rez | src/rez/vendor/version/version.py | Python | lgpl-3.0 | 46,686 | [
"VisIt"
] | 535d8926d4e07e37a70b21f15126dded2120619fa14aa0671b6c5217f2c308b7 |
#!/usr/bin/python
from brian import *
import pylab
import numpy
import scipy
import scipy.optimize
from Model import *
reference_params = {'gNa': 28, 'C': 21, 'ENa': 50, 'EK':-85, 'EL': -65, 'gK': 11.2, 'gL': 2.8,
'theta_m': -34, 'sigma_m': -5, 'tau_ma': 0.1,
'theta_n': -29, 'sigma_n': -4, 'tau_na': 10... | Aydarkhan/bursting_hh | ex1.py | Python | gpl-2.0 | 2,041 | [
"Brian"
] | b01ca6d0d300756021eabf10680854ef6ca09e954179a921f11d2f6c414b4b77 |
import os.path
import warnings
from glob import glob
from io import BytesIO
from numbers import Number
from pathlib import Path
from textwrap import dedent
from typing import (
TYPE_CHECKING,
Callable,
Dict,
Hashable,
Iterable,
Mapping,
Tuple,
Union,
)
import numpy as np
from .. import... | shoyer/xarray | xarray/backends/api.py | Python | apache-2.0 | 50,649 | [
"NetCDF"
] | 6f175f68b5caae8447f3736650244f7121fbe66096e7f34a154b4523c6537052 |
class NodeVisitor(object):
def visit(self, node):
method_name = 'visit_' + type(node).__name__
visitor = getattr(self, method_name, self.generic_visit)
return visitor(node)
def generic_visit(self, node):
raise Exception('No visit_{} method'.format(type(node).__name__))
| doubledherin/my_compiler | node_visitor.py | Python | mit | 311 | [
"VisIt"
] | 93276c3c81f4c00f9fbc3fdea3ff0c42ea60a1adaff4930cb2c655072ac7a274 |
# coding: utf-8
# Copyright (c) Henniggroup.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
"""
reads in vasprun.xml file and plots the density of states
"""
# To use matplotlib on Hipergator, uncomment the following 2 lines... | henniggroup/MPInterfaces | examples/dos.py | Python | mit | 925 | [
"VASP",
"pymatgen"
] | 87b90121fe71e412a3136e6814ff0acbf71b6da8d661dfed291f9f65850ccaaa |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
#
# License: BSD (3-clause)
from .externals.six import string_types
import numpy as np
import os
import os.path as op
from scipy import sparse, linalg
from scipy.spatial.distance import cdist
f... | effigies/mne-python | mne/source_space.py | Python | bsd-3-clause | 91,787 | [
"Mayavi"
] | 3dfe9c324fdf724af6f7cf32e9d3215341f5e9a360de051b221afd06b3b23fa7 |
# -*- coding: utf-8 -*-
# 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 y... | jat255/hyperspy | hyperspy/utils/peakfinders2D.py | Python | gpl-3.0 | 20,084 | [
"Gaussian"
] | 35861865234cd3b2bc5d0ca336de7fb6a63c70140ce9cfe9d1663de0a771d22e |
""" Class that contains client access to the transformation DB handler. """
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import six
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Base.Client import Client, createClient
from ... | ic-hep/DIRAC | src/DIRAC/TransformationSystem/Client/TransformationClient.py | Python | gpl-3.0 | 25,787 | [
"DIRAC"
] | 3873ffff7bd4da954cf2742c4707bac5c060254e0798a9d6da7170f077ebf53d |
from sys import argv
from ase.lattice.surface import hcp0001, add_adsorbate
from ase.constraints import FixAtoms
from ase.optimize.lbfgs import LBFGS
from gpaw import GPAW, Mixer, FermiDirac
tag = 'Ru001'
adsorbate_heights = {'H': 1.0, 'N': 1.108, 'O': 1.257}
slab = hcp0001('Ru', size=(2, 2, 4), a=2.72, c=1.58*2.72,... | robwarm/gpaw-symm | gpaw/test/big/Ru001/ruslab.py | Python | gpl-3.0 | 967 | [
"ASE",
"GPAW"
] | 4b0904dbd957bee51186771bfdfdb2cfef6c7ab10ffdc677ff4da9bce8d296e9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
This program is part of pygimli
Visit http://www.resistivity.net for further information or the latest version.
"""
import sys
from os import system
try:
import pygimli as pg
except ImportError:
sys.stderr.write('ERROR: cannot import the library pygimli.'+ \
... | florian-wagner/gimli | python/apps/app_template.py | Python | gpl-3.0 | 777 | [
"VisIt"
] | 487376458d0b8651364f56244e5f05d8d457b63a33b51b0064a392c802cfe3ea |
"""
Computational Neurodynamics
Exercise 2
Simulates two layers of Izhikevich neurons. Layer 0 is stimulated
with a constant base current and layer 1 receives synaptic input
of layer 0.
(C) Murray Shanahan et al, 2015
"""
from ConnectQIF2L import ConnectQIF2L
import numpy as np
import matplotlib.pyplot as plt
N1 = ... | pmediano/ComputationalNeurodynamics | Fall2015/Exercise_2/Solutions/RunQIF2L.py | Python | gpl-3.0 | 1,888 | [
"DIRAC",
"NEURON"
] | ee8a99093d5a695730fc49d32a37f47313d9835ca69209a41bd27d52de86176f |
# -*- coding: utf-8 -*-
# enzyme - Video metadata parser
# Copyright 2011-2012 Antoine Bertin <diaoulael@gmail.com>
# Copyright 2003-2006 Dirk Meyer <dischi@freevo.org>
#
# This file is part of enzyme.
#
# enzyme is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public Lice... | Branlala/docker-sickbeardfr | sickbeard/lib/enzyme/fourcc.py | Python | mit | 31,535 | [
"CRYSTAL"
] | d88b7dc0a42f79ffdbc58fb0223a5c80bfff854c492f18cabd18140a5afff22d |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import gzip
import os
import re
import sys
import tarfile
from six.moves import urllib
import tensorflow as tf
from preprocessing import preprocess_utility as ult
from datasets.imagenet_dataset import Imagene... | Aaron-Zhao123/nn_library | model_wrapper.py | Python | mit | 6,816 | [
"Gaussian"
] | 0de6ac1fc70f38e8d34ce1fb4c03af741022855060ac07892218b0c38a305aa8 |
# vim: ft=python fileencoding=utf-8 sts=4 sw=4 et:
# Copyright 2014-2018 Florian Bruhin (The Compiler) <mail@qutebrowser.org>
#
# This file is part of qutebrowser.
#
# qutebrowser 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 S... | airodactyl/qutebrowser | scripts/dev/pylint_checkers/qute_pylint/settrace.py | Python | gpl-3.0 | 1,643 | [
"VisIt"
] | 49202125de6910d3172af6aa16d137cb4351cbed0fe5e0537239b63101b807ea |
"""
nflgame is an API to retrieve and read NFL Game Center JSON data.
It can work with real-time data, which can be used for fantasy football.
nflgame works by parsing the same JSON data that powers NFL.com's live
GameCenter. Therefore, nflgame can be used to report game statistics while
a game is being played.
The p... | onebitbrain/nflgame | nflgame/__init__.py | Python | unlicense | 19,236 | [
"VisIt"
] | 1a182a4f5817b0d090568a3f462d97ab4f886f3c5573b7e714cc7c110d12e2fc |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
"""Execute computations asynchronously using threads or processes."""
__author__ = 'Brian Quinlan (brian@sweetapp.com)'
from base import (FIRST_COMPLETED,
FIRST_EXCEPTION,
... | mj3-16/mjtest | mjtest/util/concurrent/futures/__init__.py | Python | mit | 742 | [
"Brian"
] | 796daa7aa66995ea023031ed3e1266377b333d8c9e19fc501e2303f40082967a |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""Extension for flake8 to test for certain __future__ imports"""
from __future__ import print_function
import optparse
import sys
from collections import namedtuple
try:
import argparse
except ImportError as e:
argparse = e
from ast import NodeVisitor, Str, Module,... | xZise/flake8-future-import | flake8_future_import.py | Python | mit | 7,786 | [
"VisIt"
] | 240962399b2c3b1531a1bb75bdc8554f2c0000a56e0461f482edaf969f19ed3c |
##############################################################################
# Copyright (c) 2000-2016 Ericsson Telecom AB
# All rights reserved. This program and the accompanying materials
# are made available under the terms of the Eclipse Public License v1.0
# which accompanies this distribution, and is available ... | BenceJanosSzabo/titan.core | etc/autotest/titan_publisher.py | Python | epl-1.0 | 58,576 | [
"VisIt"
] | f9dcd01076aeadb1532d17b7fa0efc29a7caaa17d6728a5a6c06dc730a7e86f2 |
# Copyright (C) 2004-2011 Jakob Schiotz and Center for Individual
# Nanoparticle Functionality, Department of Physics, Technical
# University of Denmark. Email: schiotz@fysik.dtu.dk
#
# This file is part of Asap version 3.
#
# This program is free software: you can redistribute it and/or
# modify it under the terms of... | auag92/n2dm | Asap-3.8.4/Python/asap3/__init__.py | Python | mit | 5,307 | [
"ASE",
"OpenKIM"
] | 905d7b6ef15ed32a12a5139cbdb27aacd375dc4599cca8bbd9766a7c85c69983 |
"""
@name: Modules/House/_test/test_house.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2013-2020 by D. Brian Kimmel
@license: MIT License
@note: Created on Apr 8, 2013
@summary: Test handling the information for a house.
Passed all 11 tests - DBK - 2020-01-27
"""
fr... | DBrianKimmel/PyHouse | Project/src/Modules/House/_test/test_house.py | Python | mit | 3,437 | [
"Brian"
] | 8bfe0f5c7bacddbe77452ead2550182651e43ea35b63b7db8e48fae47cef0595 |
#
# Copyright 2013 Quantopian, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in wr... | wavelets/zipline | tests/test_perf_tracking.py | Python | apache-2.0 | 47,497 | [
"COLUMBUS"
] | dcd4a101ee05caa7ed50869e6deb007425705a5d3b142871ee01c9f2057cdc02 |
# Perovskites octahedral tilting extraction
# based on Surf.Sci.602 3674 (2008)
# http://dx.doi.org/10.1016/j.susc.2008.10.002
# Author: Evgeny Blokhin
#
# KNOWN BUG: in some low-symmetry cases ("batio3_lda_hw12d_160_to.out"),
# octahedra are not adjusted with the axes, and their distortion origin is unknown.
# Even i... | tilde-lab/tilde | tilde/apps/perovskite_tilting/perovskite_tilting.py | Python | mit | 17,287 | [
"ASE"
] | cd49d5594d1c84c8d9976bd8418027aa98f90737d8e5097b64f3a24184c72bfc |
"""
Author: Ben Dudson, Department of Physics, University of York
benjamin.dudson@york.ac.uk
Edward Blair, Peter Hill, John Wilson
This file is part of PyXPad.
PyXPad 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 S... | bendudson/pyxpad | pyxpad/pyxpad.py | Python | gpl-3.0 | 44,509 | [
"NetCDF"
] | b7500d8d146e89196674b53a4ed08d6a45431f6525857ad00ce8676e0ea521e3 |
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import os
class Vasp(MakefilePackage):
"""
The Vienna Ab initio Simulation Package (VASP)
... | iulian787/spack | var/spack/repos/builtin/packages/vasp/package.py | Python | lgpl-2.1 | 5,921 | [
"VASP"
] | 255ce39f35550953087bb869c47e492528deb31affc83eb4e7eb4b0ab130b3e0 |
from ase import Atoms
from ase.constraints import FixLinearTriatomic
from ase.calculators.acn import (ACN, m_me,
r_mec, r_cn)
from ase.md import Langevin
import ase.units as units
from ase.io import Trajectory
import numpy as np
pos = [[0, 0, -r_mec],
[0, 0, 0],
[0, 0, ... | miroi/open-collection | theoretical_chemistry/software_runs/ase/runs/acn_equil/acn_equil.py | Python | mit | 2,006 | [
"ASE"
] | 7b542121e60607e1f35d1bac6e193889dd7eaa43c53abc8d6d6c647f6c4d415c |
from datetime import datetime
import logging
from django.core.urlresolvers import reverse
from django.utils import html
from django.utils.translation import ugettext as _, ugettext_noop
import json
from corehq.apps.api.es import ReportCaseES
from corehq.apps.cloudcare.api import get_cloudcare_app, get_cloudcare_form_... | puttarajubr/commcare-hq | custom/succeed/reports/patient_task_list.py | Python | bsd-3-clause | 14,071 | [
"VisIt"
] | da13d3059c5baba56083fa76ad97d60f0513e7c50f2827f011ec77d812258f91 |
# -*- coding: utf-8 -*-
import numpy as np
from dipy.reconst.multi_voxel import multi_voxel_fit
from dipy.reconst.base import ReconstModel, ReconstFit
from dipy.reconst.cache import Cache
from scipy.special import hermite, gamma, genlaguerre
from scipy.misc import factorial, factorial2
from dipy.core.geometry import ca... | villalonreina/dipy | dipy/reconst/mapmri.py | Python | bsd-3-clause | 75,106 | [
"Gaussian"
] | cd2f2ba7ef5beabbdb51815cdebea9f458a82a2a16fe45abee88428b88cc5ee6 |
"""
A module that defines all SIESTA files known
"""
from copy import deepcopy
import sids.simulation as _sim
import sids.siesta.io as _sio
import sids.es as _es
import sids.helper.units as _unit
import sids.k as _k
import numpy as _np
import sparse as spar
class SparseMatrixError(Exception):
"""
Error handle... | zerothi/siesta-es | sids/siesta/files.py | Python | gpl-3.0 | 10,999 | [
"SIESTA"
] | 66a0fa5ec2430a94f494dfb9b24e5c8f1de5f93f9daf101f46d515f8fdaea362 |
from cmath import exp
from curses.ascii import SO
class Solution:
def shortestPathLength(self, graph: list[list[int]]) -> int:
memo, final, steps = set(), (1 << len(graph)) - 1, 0
queue = [(i, 1 << i) for i in range(len(graph))]
while True:
new = []
for node, state ... | l33tdaima/l33tdaima | p847h/shorest_path_length.py | Python | mit | 939 | [
"VisIt"
] | 4d0902372c170bd4cf751570d6d3332af7583b6be0636465e14875e5ac30396a |
"""Install next gen sequencing analysis tools not currently packaged.
"""
import os
import re
from fabric.api import *
from fabric.contrib.files import *
import yaml
from shared import (_if_not_installed, _make_tmp_dir,
_get_install, _get_install_local, _make_copy, _configure_make,
... | heuermh/cloudbiolinux | cloudbio/custom/bio_nextgen.py | Python | mit | 33,357 | [
"Bowtie"
] | a7e995bfaa3aced25a091e65c9396e8417ee21fa6cc70e3d2e4520885661552f |
# Copyright 2013 by Leighton Pritchard. 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.
"""This module provides classes to represent a KGML Pathway Map.
The KGML definition is ... | zjuchenyuan/BioWeb | Lib/Bio/KEGG/KGML/KGML_pathway.py | Python | mit | 28,379 | [
"Biopython"
] | eb9062c37013763be7dd7db7a34551d338a8433e8c26002c7514b7a87abc6e6b |
""" BaseHistoryCorrector is a base class for correctors of user shares within
a given group based on the history of the resources consumption
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import time as nativetime
from DIRAC im... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/private/correctors/BaseHistoryCorrector.py | Python | gpl-3.0 | 8,418 | [
"DIRAC"
] | 01fe56ddf71f76d00ab42cd14eb6a09738690057c339ff699d032e5abd018a24 |
# -*- coding: utf-8 -*-
"""
Created on Fri Nov 17 14:10:58 2017
@author: tkc
"""
import os
import pandas as pd
from tkinter import filedialog
AESQUANTPARAMFILE='C:\\Users\\tkc\\Documents\\Python_Scripts\\Augerquant\\Params\\AESquantparams.csv'
class AESspectrum():
''' Single instance of AES spectra file created f... | tkcroat/Augerquant | Modules/AES_data_classes.py | Python | mit | 7,411 | [
"Gaussian"
] | ddd450040237c91bb21b20449ce6e3880f4910fc5ecb7b88cd77de89e657fc11 |
# -*- coding: utf-8 -*-
#
# Copyright © 2009-2010 Pierre Raybaut
# Licensed under the terms of the MIT License
# (see spyderlib/__init__.py for details)
"""Utilities and wrappers around inspect module"""
import inspect
import re
# Local imports:
from SMlib.utils import encoding
SYMBOLS = r"[^\'\"a-zA-... | koll00/Gui_SM | SMlib/utils/dochelpers.py | Python | mit | 10,892 | [
"VTK"
] | de100036c8f6b7e8ffdb5cbf1a6ca6b395e599bad7de1da166bf26783c7729b8 |
# Copyright (c) 2003-2013 LOGILAB S.A. (Paris, FRANCE).
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
# 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 ... | lukaszpiotr/pylama_with_gjslint | pylama/checkers/pylint/checkers/exceptions.py | Python | lgpl-3.0 | 10,006 | [
"VisIt"
] | df8bf2d78bca24aeac0965ddf879aeb94aa95a814cfae0c2c45a26ad8a870e99 |
#
# Copyright 2015 by Justin MacCallum, Alberto Perez, Ken Dill
# All rights reserved
#
from .openmm_runner import OpenMMRunner
class ReplicaRunner(object):
def initialize(self):
pass
def minimize_then_run(self, state):
pass
def run(self, state):
pass
def get_energy(self, s... | laufercenter/meld | meld/system/runner.py | Python | mit | 1,159 | [
"OpenMM"
] | 1247875182fb794e2df4a8a6e34d2bb4938e48663817636c5624dead586b55f3 |
########################################################################
# $HeadURL$
# File : BOINCComputingElement.py
# Author : J.Wu
########################################################################
""" BOINC Computing Element
"""
__RCSID__ = "$Id$"
from DIRAC.Resources.Computing.ComputingElement ... | avedaee/DIRAC | Resources/Computing/BOINCComputingElement.py | Python | gpl-3.0 | 13,464 | [
"DIRAC"
] | 46b049e022bdea7d3444fb8e6ca379325a75132e3b43422b20f0cfd4737a4c06 |
"""
@name: Modules/Computer/Nodes/node_status.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2016-2020 by D. Brian Kimmel
@note: Created on Jul 15, 2016
@license: MIT License
@summary: Periodically check the other nodes and:
Send alerts when things happe... | DBrianKimmel/PyHouse | Project/src/Modules/Computer/Nodes/node_status.py | Python | mit | 445 | [
"Brian"
] | 123a2b5f489ac7ef74f75b09a89fa39a5e5350d0c00090e79b0fe0d987562e58 |
# 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... | pkreissl/espresso | testsuite/python/linear_momentum_lb.py | Python | gpl-3.0 | 2,919 | [
"ESPResSo"
] | 4ce4f74d18ff382675b6ce8be275e04567f52bf2e27b0c141db756eeaa320a98 |
##############################################################################
# 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... | lgarren/spack | var/spack/repos/builtin/packages/r-genomicalignments/package.py | Python | lgpl-2.1 | 2,452 | [
"Bioconductor"
] | b5284c3b1a10ca50a3611d02e94f5667f321e0a4a6ae4ae746c433a928f2db42 |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* 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
... | nuclear-wizard/moose | python/chigger/tests/edge/edge.py | Python | lgpl-2.1 | 1,051 | [
"MOOSE",
"VTK"
] | a46bbc55455862351e2ad8df4106107df0d186b8813ee60a3bf27bfb534e7125 |
###########################################################################
#
# 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/l... | google/starthinker | starthinker_ui/recipe/dag.py | Python | apache-2.0 | 5,492 | [
"VisIt"
] | 1b60f94873430a111972501a8e2441524678be5e2a35be3dbbafa7def3979b03 |
##############################################################################
# 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... | lgarren/spack | var/spack/repos/builtin/packages/py-espressopp/package.py | Python | lgpl-2.1 | 3,451 | [
"ESPResSo"
] | aa48b1126dfcbe30ff21e2a63863ae3b07ee44dcdaec5e96dd7051fc385507f2 |
# -*- coding: utf-8 -*-
"""
The :mod:`sklearn.naive_bayes` module implements Naive Bayes algorithms. These
are supervised learning methods based on applying Bayes' theorem with strong
(naive) feature independence assumptions.
"""
# Author: Vincent Michel <vincent.michel@inria.fr>
# Minor fixes by Fabian Pedre... | xuewei4d/scikit-learn | sklearn/naive_bayes.py | Python | bsd-3-clause | 49,553 | [
"Gaussian"
] | 165477d6889b76cd806487c29c48813f298830441be5d0976f9befee787b2ec8 |
#!/usr/bin/env python
#
# License: BSD
# https://raw.githubusercontent.com/stonier/py_trees/devel/LICENSE
#
##############################################################################
# Documentation
##############################################################################
"""
The core behaviour template. Al... | stonier/py_trees_suite | py_trees/behaviour.py | Python | bsd-3-clause | 12,296 | [
"VisIt"
] | 30d6fefa17a877ea8561b7b30cbae045977d69e07ba883484353752c697dd428 |
import os
os.environ['ETS_TOOLKIT'] = 'qt4'
os.environ['QT_API'] = 'pyqt'
import numpy as np
import sympy as sp
import networkx as nx
import itertools as it
from pyface.qt import QtGui, QtCore
from traits.api import HasTraits, Instance, on_trait_change
from traitsui.api import View, Item
from mayavi.core.ui.api import ... | syamajala/geodesic | geodesic.py | Python | gpl-2.0 | 8,162 | [
"Mayavi"
] | b264e1adf99fc9de9d4fc77650f423e3cf1237a04f0188d2d1e807aa8b700267 |
# -*- coding: utf-8 -*-
#
# BrodyHopfield.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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, ... | obreitwi/nest-simulator | pynest/examples/BrodyHopfield.py | Python | gpl-2.0 | 3,850 | [
"Gaussian",
"NEURON"
] | f953de862524d61df9531024c940d2eaa6d87ff2d7e67a34e450b4159a1c4ea9 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
# Denis A. Engemann <denis.engemann@gmail.com>
#
# License: BSD (3-clause)
import copy as cp
from distutils.version import LooseVersion
import itertools as itt
from math import log
imp... | wronk/mne-python | mne/cov.py | Python | bsd-3-clause | 75,382 | [
"Gaussian"
] | 1507b7d8617241dc15af347e89efaf31c064f3b4f21822a1f704bf4a39d5ca52 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import re
import logging
import os
import numpy as np
import math
from monty.io import zopen
from monty.json import jsanitize
from monty.json import MSONable
from pymatgen.core import Molecule
from pymatgen.a... | dongsenfo/pymatgen | pymatgen/io/qchem/outputs.py | Python | mit | 31,716 | [
"Q-Chem",
"pymatgen"
] | 9a17dad3cbef1076ebac99b6939ad605158a9fbcfc0e972cf7fd79c9de2bb06c |
# Copyright 2010 The Closure Library 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 a... | bjohare/cloughjordan.ie | wp-content/themes/outreach-pro/api/OpenLayers-2.13.1/tools/closure_library_jscompiler.py | Python | cc0-1.0 | 2,337 | [
"VisIt"
] | 765efb4a07c1969e2f31ecd5148ee922d522a09d108faa1082d6f856a082463b |
from __future__ import unicode_literals
import base64
import datetime
import hashlib
import json
import netrc
import os
import re
import socket
import sys
import time
import xml.etree.ElementTree
from ..compat import (
compat_cookiejar,
compat_cookies,
compat_getpass,
compat_HTTPError,
compat_http... | eric-stanley/youtube-dl | youtube_dl/extractor/common.py | Python | unlicense | 57,102 | [
"VisIt"
] | f647f7484cb2e385c283bbae02301f20e5cda8dab9447dd68f0dbc7a4b377bb6 |
#!/usr/bin/env python3
# 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 appl... | kubernetes/repo-infra | hack/verify_boilerplate.py | Python | apache-2.0 | 7,790 | [
"VisIt"
] | 6928a807e2ffc2e6902de705ce7a7cddbbbf5ef61a43901432c4f4551b4e9a7b |
from numpy import pi, sqrt, sin, cos, tan
#
# Based on "Redfearn's" formula from the The GDA Technical Manual
# http://www.icsm.gov.au/gda/gdatm/
#
# some ellipsoids
# Semi major axis Inverse flattening Central Scale factor
# GRS80 6378137.0 298.257222101 0.9996
# WGS84 6378137.0 298.25... | CanberraUAV/cuav | cuav/uav/geo.py | Python | gpl-3.0 | 4,936 | [
"Psi4"
] | c8dc544a3b8ff99cc5ae3a6c0845ab688f1083a711ff81cba105f95f03958914 |
from pycp2k.inputsection import InputSection
from ._each255 import _each255
class _wannier901(InputSection):
def __init__(self):
InputSection.__init__(self)
self.Section_parameters = None
self.Add_last = None
self.Common_iteration_levels = None
self.Filename = None
... | SINGROUP/pycp2k | pycp2k/classes/_wannier901.py | Python | lgpl-3.0 | 1,288 | [
"Wannier90"
] | 95072b25cf5c3b17297b606c95802561fe39cbffb7327c5bdf6a67eb5df4e38f |
# 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... | quang-ha/lammps | tools/python/pizza/cfg.py | Python | gpl-2.0 | 6,108 | [
"LAMMPS"
] | 5f42a61b4a92182e1412eb57e76d454fbbe00f6990dc537dea94ebf2c4f77a39 |
import unittest, re, sys
sys.path.extend(['.','..','py'])
import h2o, h2o_cmd, h2o_hosts, h2o_import as h2i
print "FIX!: Avoiding an RF histogram assertion error on some of these datasets"
DO_RF = False
class Basic(unittest.TestCase):
def tearDown(self):
h2o.check_sandbox_for_errors()
@classmethod
... | woobe/h2o | py/testdir_single_jvm/test_parse_many_doublesp_fvec.py | Python | apache-2.0 | 7,703 | [
"Dalton"
] | f20ad86b1f81dc30783292774942a46630b25225efa6d7053466381ec8e11639 |
# Copyright 2014 Pants project contributors (see CONTRIBUTORS.md).
# Licensed under the Apache License, Version 2.0 (see LICENSE).
from textwrap import dedent
from pants.backend.docgen.targets.doc import Page, Wiki, WikiArtifact
from pants.base.build_environment import get_buildroot
from pants.build_graph.address imp... | tdyas/pants | tests/python/pants_test/backend/docgen/targets/test_wiki_page.py | Python | apache-2.0 | 5,528 | [
"exciting"
] | cb822249a8165903a2a34e0641f691b8be7076353e1d83cb484379c5f625e809 |
#!/usr/bin/env python3
# @package adjust_timeline
# \author Andy Aschwanden, University of Alaska Fairbanks, USA
# \brief Script adjusts a time axis of a file.
# \details Script adjusts the time axis of a file.
# Say you have monthly climate forcing from 1980-1-1 through 2001-1-1 in
# the forcing file foo_1980-1999.n... | pism/pism | util/adjust_timeline.py | Python | gpl-3.0 | 5,319 | [
"NetCDF"
] | 6600c5896f8cbeb00c6ac9d3dcdaa3d4eae7b9d23f2a241808706d135d6a8a5d |
# This code is part of Ansible, but is an independent component.
# This particular file snippet, and this file snippet only, is BSD licensed.
# Modules you write using this snippet, which is embedded dynamically by Ansible
# still belong to the author of the module, and may assign their own license
# to the complete wo... | supertom/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 85,059 | [
"VisIt"
] | 69fb4d3b8e552715702cfe3ad850a385f0d82cb2cc01db10d4832d5928d4bf32 |
#!/usr/bin/env python
"""
Originally written by Kelly Vincent
pretty output and additional picard wrappers by Ross Lazarus for rgenetics
Runs all available wrapped Picard tools.
usage: picard_wrapper.py [options]
code Ross wrote licensed under the LGPL
see http://www.gnu.org/copyleft/lesser.html
"""
import optparse, o... | jhl667/galaxy_tools | tools/picard/picard_wrapper_old.py | Python | apache-2.0 | 36,790 | [
"Galaxy",
"pysam"
] | 42c540c300ed549bf18b20ab19d93703ca9bc9b0f23734f78bb39e032f4a88c3 |
from django import forms
from osp.visits.models import Visit
from django.conf import settings
class VisitForm(forms.ModelForm):
reason = forms.MultipleChoiceField(choices=settings.VISIT_REASON_CHOICES)
class Meta:
model = Visit
exclude = ('student', 'submitter',)
widgets = {
... | mariajosefrancolugo/osp | osp/visits/forms.py | Python | lgpl-3.0 | 831 | [
"VisIt"
] | da88d4754290f06c93e68abf10654afa658f7c0d5ce9f004d4986def613dc9cf |
# Author: David Goodger
# Contact: goodger@users.sourceforge.net
# Revision: $Revision$
# Date: $Date$
# Copyright: This module has been placed in the public domain.
"""
Transforms for CSEP processing.
- `Headers`: Used to transform a CSEP's initial RFC-2822 header. It remains a
field list, but some entries get pr... | crystalspace/CS | docs/support/cseptools/cseps.py | Python | lgpl-2.1 | 11,118 | [
"CRYSTAL"
] | 8a464bec42f303e973254811c0c4630de56143b3f4665fed3251d4a1a99cf442 |
"""Validate dependencies."""
from __future__ import annotations
import ast
from pathlib import Path
from homeassistant.const import Platform
from homeassistant.requirements import DISCOVERY_INTEGRATIONS
from .model import Integration
class ImportCollector(ast.NodeVisitor):
"""Collect all integrations reference... | rohitranjan1991/home-assistant | script/hassfest/dependencies.py | Python | mit | 8,544 | [
"VisIt"
] | 52661824421e4e264349b29e94910d762fe99d796a53f7ce427e2aa7757f78e4 |
import re
import sys
from setlx2py.setlx_ast import *
from setlx2py.setlx_parser import Parser
TAG_INTERPOLATION = "KLIENTERPOLATION"
class AstTransformer(NodeVisitor):
def visit(self, node, parent=None):
""" Visit a node.
"""
method = 'visit_' + node.__class__.__name__
visitor =... | Rentier/setlx2py | setlx2py/setlx_ast_transformer.py | Python | apache-2.0 | 2,965 | [
"VisIt"
] | 36e1806033b26ae54793ac8519427fb26e676419eafaf8b1ce2c32a0b0b1232f |
from __future__ import unicode_literals
import re
from .common import InfoExtractor
from ..compat import (
compat_urllib_parse,
compat_urllib_request,
)
from ..utils import (
clean_html,
ExtractorError,
determine_ext,
)
class XVideosIE(InfoExtractor):
_VALID_URL = r'https?://(?:www\.)?xvideo... | apllicationCOM/youtube-dl-api-server | youtube_dl_server/youtube_dl/extractor/xvideos.py | Python | unlicense | 2,573 | [
"Galaxy"
] | 0e6920744b39276e133b147b9629cf023c43ffaed22032afcdd8480a22e35b25 |
"""
Implementation of Regression on Order Statistics for imputing left-
censored (non-detect data)
Method described in *Nondetects and Data Analysis* by Dennis R.
Helsel (John Wiley, 2005) to estimate the left-censored (non-detect)
values of a dataset.
Author: Paul M. Hobson
Company: Geosyntec Consultants (Portland, ... | bert9bert/statsmodels | statsmodels/imputation/ros.py | Python | bsd-3-clause | 19,099 | [
"Gaussian"
] | 9dbc4838cd50db76a74c8acff5880141fe3895a30743089ef0f4bba16d26e6a2 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkGeometryFilter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk... | chrisidefix/devide | modules/vtk_basic/vtkGeometryFilter.py | Python | bsd-3-clause | 488 | [
"VTK"
] | 383b6d7453c7921c38eccb7e4d27f785b63d714e6a43ffac5bd75ce0c2f3779a |
"""
Instructor Dashboard Views
"""
import logging
import datetime
from opaque_keys import InvalidKeyError
from opaque_keys.edx.keys import CourseKey
import uuid
import pytz
import mimetypes
import json
import pdb
import os
import hashlib
from django.contrib.auth.decorators import login_required
from django.views.deco... | MakeHer/edx-platform | lms/djangoapps/instructor/views/instructor_dashboard.py | Python | agpl-3.0 | 52,947 | [
"VisIt"
] | fa0f286da66df963d6c07a5275f96a9c48e58712671bc1d9c088bd389cae7c1e |
'''
Created on Jul 22, 2011
@author: mkiyer
'''
'''
Created on Jan 30, 2011
@author: mkiyer
chimerascan: chimeric transcript discovery using RNA-seq
Copyright (C) 2011 Matthew Iyer
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published... | tectronics/chimerascan | chimerascan/deprecated/nominate_spanning_reads_v03.py | Python | gpl-3.0 | 3,971 | [
"pysam"
] | ecfecb548150a81936e6fc9e041fff37d88477939c94547e4239d39e80b1f2f9 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""Unit tests for data_ingestion.py script."""
#
# (C) Pywikibot team, 2012-2015
#
# Distributed under the terms of the MIT license.
#
from __future__ import unicode_literals
__version__ = '$Id$'
import os
from tests import _data_dir
from tests import _images_dir
from tests.... | emijrp/pywikibot-core | tests/data_ingestion_tests.py | Python | mit | 3,897 | [
"CRYSTAL"
] | cd9271c965fa2e10f16948d6703c245a0a6156d99171d4fd8d60e3dc327debcb |
""" Test_RSS_Policy_DTPolicy
"""
__RCSID__ = '$Id: $'
from mock import MagicMock
import unittest
from DIRAC import gLogger
import DIRAC.ResourceStatusSystem.Policy.DowntimePolicy as moduleTested
################################################################################
class DTPolicy_TestCase( unittest.Test... | andresailer/DIRAC | ResourceStatusSystem/Policy/test/Test_RSS_Policy_DTPolicy.py | Python | gpl-3.0 | 3,951 | [
"DIRAC"
] | 4e453ac4dda44431f015cfbfeab0de21c395ae841ab61497044082abc2449c20 |
# 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.
#
"""Implement Roulette Wheel selection on a population.
This implements Roulette Wheel selection in which individuals are
selected from a population ... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/GA/Selection/RouletteWheel.py | Python | gpl-2.0 | 4,824 | [
"Biopython"
] | f5d7b954cb2403eda253bad707c936b2cfafdf33a8e53da0907b9a87149e5b53 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-get-pilot-logging-info.py
# Author : Stuart Paterson
########################################################################
"""
Retrieve logging info of a Grid pilot
Usage:
dirac-admin-get-pilot-... | yujikato/DIRAC | src/DIRAC/Interfaces/scripts/dirac_admin_get_pilot_logging_info.py | Python | gpl-3.0 | 2,247 | [
"DIRAC"
] | b68afa798d596070af18e5dc1162c16cdc63158715f93f5c4341f04115ca94bc |
"""
Structure connectivity class.
"""
import collections
import logging
import networkx as nx
import numpy as np
from monty.json import MSONable, jsanitize
from pymatgen.analysis.chemenv.connectivity.connected_components import (
ConnectedComponent,
)
from pymatgen.analysis.chemenv.connectivity.environment_nodes... | materialsproject/pymatgen | pymatgen/analysis/chemenv/connectivity/structure_connectivity.py | Python | mit | 16,317 | [
"pymatgen"
] | 432c8a285d4a364afdc24300d96721d90859763464adb08452ef7b239ee14743 |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# (c) 2015 Toshio Kuratomi <tkuratomi@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either... | dlazz/ansible | lib/ansible/executor/module_common.py | Python | gpl-3.0 | 41,164 | [
"VisIt"
] | 09c6b457894c5f198e5ec99769e6908b1b09f5f6930ccf37d0ae3f60b916a590 |
# (c) 2012, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any lat... | jaddison/ansible | lib/ansible/template/safe_eval.py | Python | gpl-3.0 | 4,160 | [
"VisIt"
] | 640c3a818fe68523ccbe794289f335a846b2995a8beeab2be74ba58b2faaa43c |
'''
WebdriverWrapper Module
This module wraps Selenium Webdriver, and provides a cleaner, more consistent interface. It also provides error
handling, and creates a more deterministic tool for web automation
'''
import httplib
import logging
import signal
import os
from urlparse import urlparse, urljoin
from selenium... | Shapeways/coyote_framework | coyote_framework/webdriver/webdriverwrapper/WebDriverWrapper.py | Python | mit | 44,327 | [
"VisIt"
] | af28a6400aa28d5105d341cd113bffbee2a9e7a0e7db486344bcd14f36cd22dc |
from zope.interface import Interface
from foolscap.api import StringConstraint, ListOf, TupleOf, SetOf, DictOf, \
ChoiceOf, IntegerConstraint, Any, RemoteInterface, Referenceable
HASH_SIZE=32
SALT_SIZE=16
SDMF_VERSION=0
MDMF_VERSION=1
Hash = StringConstraint(maxLength=HASH_SIZE,
minLeng... | kytvi2p/tahoe-lafs | src/allmydata/interfaces.py | Python | gpl-2.0 | 125,772 | [
"Brian",
"VisIt"
] | 31f49afdf1ca6b247071be9b9a6957671bb8134c14a02624a127c3aff468c004 |
# PyVision License
#
# Copyright (c) 2006-2008 David S. Bolme
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, thi... | Dfred/concept-robot | HRI/vision/pyvision_0.9.0/src/pyvision/point/DetectorCorner.py | Python | gpl-3.0 | 7,990 | [
"Gaussian"
] | 86be5ad11a5e67df9721681c92f045a7458c977b75f55350c43c46226159413c |
# -----------------------------------------------------------------------------
# Copyright (c) 2014--, The Qiita Development Team.
#
# Distributed under the terms of the BSD 3-clause License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... | antgonza/qp-shotgun | qp_shogun/sortmerna/sortmerna.py | Python | bsd-3-clause | 6,980 | [
"BLAST"
] | ff7715f5f2fd16de97d8cb62a9c65c51f4246b0e4eaf1236a4a6b69a6981bc98 |
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