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# -*- coding: utf-8 -*-
"""
ASSET is a statistical method :cite:`asset-Torre16_e1004939` for the detection
of repeating sequences of synchronous spiking events in parallel spike trains.
ASSET analysis class object of finding patterns
-----------------------------------------------
.. autosummary::
:toctree: _toc... | INM-6/elephant | elephant/asset/asset.py | Python | bsd-3-clause | 102,992 | [
"NEURON"
] | 011cabc276c67e49909b2cf80965bedf52003d1b359971c65488abe7d081c24a |
#!/usr/bin/env python
"""
MODULE: r.in.narr
AUTHOR(S): Julien Seguinot <seguinot@vaw.baug.ethz.ch>.
PURPOSE: Import North American Regional Reanalysis fields from the ESRL
Physical Science Division [1] netCDF data files.
COPYRIGHT: (c) 2011-2016 Julien Seguinot
This program is free softwar... | jsegu/r.in.narr | r.in.narr.py | Python | gpl-3.0 | 2,795 | [
"NetCDF"
] | 15d7dc1ec0645f4b0243b533b4f07da1ad5e6f5bd25156411d665623bb4f90b8 |
from deepnet import util
from deepnet import deepnet_pb2
import cPickle as pickle
from choose_matrix_library import *
import glob
import numpy as np
import os.path
import scipy.sparse as sp
import pdb
import gzip
import random
class Disk(object):
"""A Disk access manager."""
def __init__(self, filenames, numdim_li... | kobiso/ControlledDropout | deepnet/datahandler.py | Python | bsd-3-clause | 26,814 | [
"Gaussian"
] | 656266b772d876ca566d101c8900761e812240d4235a918afbd4b390ce386f14 |
# VMware vSphere Python SDK
# Copyright (c) 2008-2018 VMware, Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# ... | vmware/pyvmomi | pyVmomi/VmomiSupport.py | Python | apache-2.0 | 69,928 | [
"VisIt"
] | ce58f7451309b13925f1a98729ac886414df9e64410801b82f1604816cc342af |
import pytest
import tensorflow as tf
import mdtraj as md
@pytest.fixture(scope='session')
def sess():
sess = tf.Session()
yield sess
sess.close()
@pytest.fixture()
def traj():
t = md.load('fs_peptide/trajectory-9.xtc', top='fs_peptide/fs-peptide.pdb', stride=21)
return t
| mdtraj/tftraj | tests/conftest.py | Python | mit | 297 | [
"MDTraj"
] | e728d970a9f97a1a7237caa77453ccc24da08cdabe80948d059db6a40b6ab1ea |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import warnings
import numpy as np
from math import pi
import unittest
import os
from monty.os.path import which
from pymatgen.analysis.local_env import ValenceIonicRadiusEvaluator, \
VoronoiNN, JmolNN, M... | gVallverdu/pymatgen | pymatgen/analysis/tests/test_local_env.py | Python | mit | 49,765 | [
"CRYSTAL",
"Jmol",
"Pybel",
"pymatgen"
] | eb5961ff7b2c88d48146c7debaef4e23eba8986d7ef67d5c0b6eefee4c63f0ba |
# Copyright 2000 by Bertrand Frottier . All rights reserved.
# Revisions 2005-2006 copyright Michiel de Hoon
# Revisions 2006-2009 copyright Peter Cock
# 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.... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Blast/NCBIXML.py | Python | gpl-2.0 | 24,495 | [
"BLAST",
"Biopython"
] | 60a814be3e7901a4d0c8058b7a6cf67993b2d295338bcff10907dbc45d4bd9ac |
import pyvista as pv
import pyvistaqt as pvqt
from PyQt5.QtCore import *
from PyQt5.QtGui import *
from PyQt5.QtWidgets import *
from gempy.plot._vista import Vista
class MainWindow(QMainWindow): # QtWidgets.QWidget
def __init__(self, geo_model, parent=None):
super(MainWindow, self).__init__(parent)
... | cgre-aachen/gempy | gempy/plot/vista_qt.py | Python | lgpl-3.0 | 2,552 | [
"VTK"
] | 4aef1a95b6dd93019a18e198238e6e3530dc4a9173babd30fe2c1358512fcc3b |
import numpy as np
from ase import Atoms, Atom
from ase.parallel import barrier, rank, size
from gpaw.cluster import Cluster
from gpaw.test import equal
from ase.structure import molecule
from math import pi, sqrt
R = 2.0
CO = Atoms([Atom('C', (1, 0, 0)), Atom('O', (1, 0, R))])
CO.rotate('y', pi/2)
equal(CO.position... | ajylee/gpaw-rtxs | gpaw/test/cluster.py | Python | gpl-3.0 | 2,246 | [
"ASE",
"GPAW"
] | 763ed194578099a051aedf5940846314b321fd0257a538e4093b34e832c3bd73 |
## Base goals app file
from project import Project
from places import Place
from total import Total
import sys
if __name__ == "__main__":
print ""
print "2015 Goals"
print "Goal 1: Ship 48 projects"
proj = Project()
print "Projects Shipped", ", ".join(proj.projects)
print "Projects Remain... | pursuitofepic/text-accounting | goals.py | Python | gpl-2.0 | 1,065 | [
"VisIt"
] | 74f08fc162338648fe0380db43679f1c5c4944c43966c1e89d62e56a0f751d1f |
# -*- coding: utf-8 -*-
'''
Support for nzbget
'''
# Import salt libs
import salt.utils
__func_alias__ = {
'list_': 'list'
}
def __virtual__():
'''
Only load the module if apache is installed
'''
cmd = 'nzbget'
if salt.utils.which(cmd):
return 'nzbget'
return False
def version(... | victorywang80/Maintenance | saltstack/src/salt/modules/nzbget.py | Python | apache-2.0 | 3,345 | [
"MOE"
] | 82d0efaa9fee1e43f18f5c8ebc62315461f6e460e866fbf5de6f017dba3100f6 |
#!/usr/bin/env python
import os
import sys
print '''
This file removes duplicate and common commands from ~/.bash_eternal_history and saves results in final_out.garbage
'''
cmd = ''' cat ~/.bash_eternal_history | awk '{ s = ""; for (i = 11; i <= NF; i++) s = s $i " "; print s }' > tttttttttttmp_out '''
os.system(cm... | cuixu66/dotfiles | scripts/analyze_bash_eternal_history.py | Python | gpl-2.0 | 1,869 | [
"GULP"
] | a2d921ac29adf16cb3243804e5ca8024ab0482b418a4d48587879fc8caa90671 |
# # #
# Current implementation of the cru ts31 (ts32) delta downscaling procedure
#
# Author: Michael Lindgren (malindgren@alaska.edu)
# # #
import numpy as np
def write_gtiff( output_arr, template_meta, output_filename, compress=True ):
'''
DESCRIPTION:
------------
output a GeoTiff given a numpy ndarray, rasterio... | ua-snap/downscale | snap_scripts/old_scripts/tem_iem_older_scripts_april2018/tem_inputs_iem/old_code/hur_cru_ts31_to_cl20_downscaling.py | Python | mit | 22,421 | [
"NetCDF"
] | 2b9a90a48f9f6eb77c724f7dd9c24e1b08e57cf850984a2d6d792e43b80b4854 |
#!/usr/bin/env python
import subprocess
import argparse
import sys
import os
import hashlib
import shutil
import uuid
import time
import uuid
from glob import glob
from ififuncs import hashlib_manifest
from ififuncs import get_date_modified
from premis import make_premis
from premis import write_premis
from premis impo... | kieranjol/IFIscripts | legacy_scripts/rawbatch.py | Python | mit | 15,738 | [
"Brian"
] | af92f3b0ca94b2a5c20b39881b423e639c4dbf980b3c3d86b2c7e2d16f002966 |
# Copyright 2012 by Wibowo Arindrarto. 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.
"""Tests for SearchIO HmmerIO parsers."""
import os
import unittest
from Bio import Bio... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_SearchIO_hmmer3_text.py | Python | gpl-2.0 | 108,823 | [
"BLAST",
"Biopython"
] | d9ebc5fdf735023987c62f60169a036e91857f502d62f4addddf426c3fa3161d |
##~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~#~##
## ##
## This file forms part of the Badlands surface processes modelling application. ##
## ... | badlands-model/pyBadlands | badlands/badlands/flow/visualiseFlow.py | Python | gpl-3.0 | 11,198 | [
"ParaView",
"VisIt"
] | 7b07c17f738bc68433bd3ff33571f7209d5acabfc80fa79364af4d8dc1a6406a |
# -*- coding: utf-8 -*-
# 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | sasha-gitg/python-aiplatform | tests/unit/gapic/aiplatform_v1beta1/test_vizier_service.py | Python | apache-2.0 | 163,960 | [
"Octopus"
] | f66a67bb46b65feadb19b40bd8b90112bb0d154643a796a6bdf2d83ffa9bf0ff |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import chig... | nuclear-wizard/moose | python/peacock/ExodusViewer/plugins/ColorbarPlugin.py | Python | lgpl-2.1 | 14,544 | [
"MOOSE"
] | 72cb6d084bc25ceb4e5519b4d381caa99deec828bb1f16196fb1ba202e3bc30c |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2015, 2016 CERN.
#
# Invenio 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... | lnielsen/invenio-records-rest | tests/helpers.py | Python | gpl-2.0 | 3,069 | [
"Galaxy"
] | 30fc8482039b15170e58b6d7d9846a242155862e78845b425137630b084456a2 |
# -*- coding: utf-8
# pylint: disable=line-too-long
"""Helper functions for the anvi'o snakemake workflows"""
import os
import sys
import json
import copy
import snakemake
import anvio
import anvio.utils as u
import anvio.errors as errors
import anvio.terminal as terminal
import anvio.filesnpaths as filesnpaths
from... | meren/anvio | anvio/workflows/__init__.py | Python | gpl-3.0 | 31,245 | [
"BLAST"
] | 0138d03aa5cd5915e923ebe3789434f91db296647f1e543c2257d23e8ff4014e |
# Authors: Denis Engemann <denis.engemann@gmail.com>
# License: BSD (3-clause)
import numpy as np
from scipy import stats
def find_outliers(X, threshold=3.0):
"""Find outliers based on Gaussian mixture
Parameters
----------
X : np.ndarray of float, shape (n_elemenets,)
The scores for which ... | effigies/mne-python | mne/preprocessing/bads.py | Python | bsd-3-clause | 923 | [
"Gaussian"
] | f882227e0d960c2e1ded4fdaaec86d73da7d07585934f31c8aefe4ce3dbc9892 |
import os
import sys
import pdb
import shutil
import pandas as pd
import numpy as np
import mpmath
import time
import multiprocessing as mp
import csv
import astropy.coordinates as astroCoords
import astropy.units as u
import heapq
import pickle
from kbmodpy import kbmod as kb
from astropy.io import fits
from astropy.w... | DiracInstitute/kbmod | analysis/analysis_utils.py | Python | bsd-2-clause | 53,993 | [
"Gaussian",
"VisIt"
] | 60bb612068713039cf971719cea679866fc51a9f87ed5c9af615bc4dff886ba0 |
# Copyright 2016 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... | hfp/tensorflow-xsmm | tensorflow/contrib/distributions/python/ops/mvn_diag.py | Python | apache-2.0 | 8,832 | [
"Gaussian"
] | d44153dba44b642711d05a031f5a4d71d9343002743ccc04b7adb20c1e73d8b4 |
#
# Copyright (c) 2009-2015, Jack Poulson
# All rights reserved.
#
# This file is part of Elemental and is under the BSD 2-Clause License,
# which can be found in the LICENSE file in the root directory, or at
# http://opensource.org/licenses/BSD-2-Clause
#
import El
m = 500
n = 1000
k = 750
testMehrotra = True
... | mcopik/Elemental | examples/interface/LPAffineDense.py | Python | bsd-3-clause | 3,445 | [
"Gaussian"
] | eb231b1e7f6cadef1e6f7fa054091911cc323bb76c2710cbcba188a184700eb7 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes for non-standard space-group settings
"""
import re
from fractions import Fraction
from typing import List, Tuple, Union
import numpy as np
from pymatgen.core import Lattice
... | gmatteo/pymatgen | pymatgen/symmetry/settings.py | Python | mit | 7,337 | [
"pymatgen"
] | 851261aff185a4ec812dc32f640bf4a6fe67b606feb00af7c7f66ac0963294c2 |
# -*- coding: utf-8 -*-
"""
<DefineSource>
@Date : Fri Nov 14 13:20:38 2014 \n
@Author : Erwan Ledoux \n\n
</DefineSource>
A Pyploter
"""
#<DefineAugmentation>
import ShareYourSystem as SYS
BaseModuleStr="ShareYourSystem.Standards.Viewers.Viewer"
DecorationModuleStr="ShareYourSystem.Standards.Classors.Classer"
SY... | Ledoux/ShareYourSystem | Pythonlogy/build/lib/ShareYourSystem/Standards/Viewers/Pyploter/__init__.py | Python | mit | 51,979 | [
"Brian"
] | 81deb0b5d957c8c8fdfd4066c95792bcf0cbf8f1e14200796c44f386b92e1176 |
import MDAnalysis
import numpy
import numpy.linalg
import math
from KabschAlign import *
from mpl_toolkits.mplot3d import Axes3D
import matplotlib.pyplot as plt
class IterativeMeansAlign(object):
def __init__(self):
"""
Constructor
"""
def iterativeMeans(self, coords, eps, maxIter):
# all coordinates are... | acadev/pyACA | src/IterativeMeansAlign.py | Python | gpl-2.0 | 2,089 | [
"MDAnalysis"
] | 0a11aa9fdd1716278c7f82b9685fcec85f86b29d8e24e203082a763ad1997062 |
#!/usr/bin/env python
# vim:fileencoding=utf-8
from __future__ import (unicode_literals, division, absolute_import,
print_function)
__license__ = 'GPL v3'
__copyright__ = '2013, Kovid Goyal <kovid at kovidgoyal.net>'
import os, re
from io import BytesIO
from functools import partial
from cali... | pra85/calibre | src/calibre/web/feeds/jsnews.py | Python | gpl-3.0 | 17,009 | [
"VisIt"
] | 182ffaf827695d0e398d3966088b35f7a7e267011e030a1aebaa5ae5f86b6d98 |
# Rekall Memory Forensics
#
# Copyright 2014 Google Inc. All Rights Reserved.
#
# 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 v... | chen0031/rekall | rekall-core/rekall/entities/query/matcher.py | Python | gpl-2.0 | 6,952 | [
"VisIt"
] | d51569c91834b255bd43191673ad4cba84a4fd508d9e1387c949fe93259990bb |
"""
Numerical python functions written for compatability with MATLAB
commands with the same names.
MATLAB compatible functions
-------------------------------
:func:`cohere`
Coherence (normalized cross spectral density)
:func:`csd`
Cross spectral density uing Welch's average periodogram
:func:`detrend`
Remov... | Solid-Mechanics/matplotlib-4-abaqus | matplotlib/mlab.py | Python | mit | 97,213 | [
"Gaussian"
] | 71e06e99a1d02fd09e680022523cc424a569ee109606babe4def7eb24fe91ae4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import pylid
from collections import Counter
pl = pylid.PyLID(3)
pl.total_ngrams = 92294471
pl.lang = 'pl'
pl.ngrams = Counter({
u'ie#': 928803,
u'nie': 914100,
u'#pr': 682852,
u'#po': 635072,
u'ch#': 597022,
u'ani': 482672,
u'#na': 449009,
... | dmort27/pylid | pylid/langs/pl.py | Python | mit | 261,872 | [
"ADF",
"ASE",
"BWA",
"EPW",
"Elk"
] | 07732c7d20a9abfb328bb1aaa65dd2bd7c6b71018115f9316abd8f8706d42d63 |
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2009 Brian G. Matherly
# Copyright (C) 2010 Douglas S. Blank
# Copyright (C) 2011-2019 Jerome Rapinat
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | gramps-project/addons-source | lxml/lxmlGramplet.py | Python | gpl-2.0 | 28,753 | [
"Brian"
] | dd22920fb2f7a27e8846e1aca7ca9794861a163b29eb1af3a8b15bfd20618473 |
#!/usr/bin/python
#
# -----------------------------------------------------------------------------
# Copyright * 2014, United States Government, as represented by the
# Administrator of the National Aeronautics and Space Administration. All
# rights reserved.
#
# The Crisis Mapping Toolkit (CMT) v1 platform is license... | nasa/CrisisMappingToolkit | setup.py | Python | apache-2.0 | 2,757 | [
"Brian"
] | cd48d0bd734f1f529ceaf3d7a0b9693546a94e8f53faef69406f633ffb21c60b |
# module pyparsing.py
#
# Copyright (c) 2003-2019 Paul T. McGuire
#
# Permission is hereby granted, free of charge, to any person obtaining
# a copy of this software and associated documentation files (the
# "Software"), to deal in the Software without restriction, including
# without limitation the rights to use, cop... | InsightSoftwareConsortium/ITKExamples | Utilities/SphinxExtensions/pyparsing/__init__.py | Python | apache-2.0 | 6,878 | [
"VisIt"
] | dba4415e6510b6f6f25b67555a95039cf3352474b8fa0a8c6b64635b88f9e022 |
#########
# firstVideo.py
# This program is part of the online PS-Drone-API-tutorial on www.playsheep.de/drone.
# It shows the general usage of the video-function of a Parrot AR.Drone 2.0 using the PS-Drone-API.
# The drone will stay on the ground.
# Dependencies: a POSIX OS, openCV2, PS-Drone-API 2.0 beta or higher.
#... | FroeMic/CDTM-Deep-Learning-Drones | src/playground/firstVideo.py | Python | mit | 2,789 | [
"VisIt"
] | 964f847275b11d95ad5090dad8bfe97fb1ad423de8f1417826be3aff2addf351 |
'''
Created on 2013-08-19
Variable and Dataset classes for handling geographical datasets.
@author: Andre R. Erler, GPL v3
'''
# numpy imports
import numpy as np
import numpy.ma as ma # masked arrays
from numpy.lib.stride_tricks import as_strided
import scipy.stats as ss
from scipy.interpolate import griddata
import... | aerler/GeoPy | src/geodata/base.py | Python | gpl-3.0 | 207,860 | [
"NetCDF"
] | d546f85d7aca6803190a40dab515b69daa2a97d686ae9006e716b83b726a6fb1 |
"""
=========================================================
Gaussian Processes regression: basic introductory example
=========================================================
A simple one-dimensional regression example computed in two different ways:
1. A noise-free case
2. A noisy case with known noise-level per ... | RPGOne/Skynet | scikit-learn-0.18.1/examples/gaussian_process/plot_gpr_noisy_targets.py | Python | bsd-3-clause | 3,706 | [
"Gaussian"
] | 31e49151725f7e448380af4746a2fc9929b437d5c8b12aa93d2c310b37b93887 |
"""
The GA4GH data model. Defines all the methods required to translate
data in existing formats into GA4GH protocol types.
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import base64
import collections
import glob
import os
import ga4gh.exceptions a... | diekhans/ga4gh-server | ga4gh/datamodel/__init__.py | Python | apache-2.0 | 15,662 | [
"pysam"
] | 1876c35965761481911d8c4fc181d27bb33b71f58dee5e69377b7d6b3ec68dee |
import itertools
import numpy as np
import mdtraj as md
import msmbuilder as msmb
trj0 = md.load("./system.subset.pdb")
trajectories = [md.load("./Trajectories/trj%d.h5" % i) for i in range(5)]
#atom_indices = np.arange(trj0.n_atoms)
atom_indices = np.array([i for i, atom in enumerate(trj0.top.atoms) if atom.element.... | choderalab/MSMs | attic/src/code/tica/test_sensitivity_tica.py | Python | gpl-2.0 | 790 | [
"MDTraj"
] | c8e19db92053818f95ded4fe15cccd3e2e448405d189dbd95d071a5151dd81f8 |
# Copyright 2017 The 'Scalable Private Learning with PATE' 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
#
# ... | tensorflow/privacy | research/pate_2018/ICLR2018/rdp_cumulative.py | Python | apache-2.0 | 12,995 | [
"Gaussian"
] | f225b72f989db65763ffce4153ae3875ce0ad82b72333a2badaaeee40fd879b5 |
''' Significant lifting from https://jmetzen.github.io/2015-11-27/vae.html '''
import time
import numpy as np
import tensorflow as tf
from tensorflow.python.ops import rnn
import random
import matplotlib.pyplot as plt
import re, string
from sklearn.feature_extraction.text import CountVectorizer
from collections impo... | dricciardelli/vae2vec | def_def_alt_oh2.py | Python | mit | 37,258 | [
"Gaussian"
] | ff2b6b7d71f5abf7e1b5b873fb8db9bf6639ea70c51343e68a3dfb6125116646 |
# -*- coding: utf-8 -*-
# This file is public domain according to its author, Brian Hsu
"""Gist directive for reStructuredText."""
import requests
from nikola.plugin_categories import ShortcodePlugin
class Plugin(ShortcodePlugin):
"""Plugin for gist directive."""
name = "gist"
def set_site(self, site... | andredias/nikola | nikola/plugins/shortcode/gist.py | Python | mit | 1,889 | [
"Brian"
] | 42ede66392f8afa9cfb1b1a10c6651de2663dfeeabdd37cbd09b37bad5863a9d |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class PyMethylcode(PythonPackage):
"""MethylCoder is a single program that takes of bisulfite-tr... | iulian787/spack | var/spack/repos/builtin/packages/py-methylcode/package.py | Python | lgpl-2.1 | 747 | [
"Bowtie"
] | 188fdb71a19c10886a9ae647d75d398681f80158ad2202aa883df5bbe22610b4 |
"""
Sphinx plugins for Django documentation.
"""
import json
import os
import re
from docutils import nodes
from docutils.parsers.rst import Directive, directives
from sphinx import addnodes
from sphinx.builders.html import StandaloneHTMLBuilder
from sphinx.domains.std import Cmdoption
from sphinx.util.console import ... | ifduyue/django | docs/_ext/djangodocs.py | Python | bsd-3-clause | 10,819 | [
"VisIt"
] | 5f17613f433a2879833aa1d8e28e812fc432bb9ea0b6e8993fb10cfc85cf2e3c |
from collections import defaultdict
from .irvisitor import IRVisitor
from .ir import *
from .block import Block
from .env import env
from .symbol import Symbol
from logging import getLogger
logger = getLogger(__name__)
class UseDefTable(object):
def __init__(self):
self._def_sym2stm = defaultdict(set)
... | ktok07b6/polyphony | polyphony/compiler/usedef.py | Python | mit | 8,622 | [
"VisIt"
] | 202ba4b9a33abbbb46a2a67a97f9c67c4787aa22c53e6012c382b91f19a25fd2 |
from __future__ import division
import keras.backend as K
import theano.tensor as T
from keras.layers import Layer, InputSpec
from keras import initializations, regularizers, constraints
import theano
import numpy as np
floatX = theano.config.floatX
class LearningPrior(Layer):
def __init__(self, nb_gau... | cvpr17-id899/saliency | gaussian_prior.py | Python | mit | 4,345 | [
"Gaussian"
] | 151eb252dfb2fe0c2ca7a0037873c2b920555d90ad4be8b51648dcef96d032a3 |
"""
Sequence Alignment
==================
"""
import logging
import os.path as op
import subprocess
import tempfile
from collections import defaultdict
from itertools import count, groupby
import numpy as np
import pandas as pd
from Bio import AlignIO
from Bio import pairwise2
from Bio.Align import MultipleSeqAlignmen... | SBRG/ssbio | ssbio/protein/sequence/utils/alignment.py | Python | mit | 28,897 | [
"Biopython"
] | efecdb721b4f61b8facc292df75b157977721835222a15702fe187b0b2edf823 |
## \file
## \ingroup tutorial_roofit
## \notebook
##
## \brief Multidimensional models: multi-dimensional p.d.f.s with conditional p.d.fs in product
##
## `pdf = gauss(x,f(y),sx | y ) * gauss(y,ms,sx)` with `f(y) = a0 + a1*y`
##
## \macro_code
##
## \date February 2018
## \authors Clemens Lange, Wouter Verkerke (C++... | karies/root | tutorials/roofit/rf305_condcorrprod.py | Python | lgpl-2.1 | 2,566 | [
"Gaussian"
] | da4eee3337d3bec86782573e874f1e9f3626136d607f7c4c60afb8e013624afd |
""" DowntimePolicy module
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = '$Id$'
from DIRAC import S_OK
from DIRAC.ResourceStatusSystem.PolicySystem.PolicyBase import PolicyBase
class DowntimePolicy(PolicyBase):
""" The DowntimePolicy ch... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Policy/DowntimePolicy.py | Python | gpl-3.0 | 1,542 | [
"DIRAC"
] | e6e262545fed0fcbfb99639a2108b5b5b8b30992bde39a117dc5c43a7602d414 |
# -*- coding: utf-8 -*-
# This file is part of MyPaint.
# Copyright (C) 2012-2015 by Andrew Chadwick <a.t.chadwick@gmail.com>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 o... | achadwick/mypaint | gui/colors/hcywheel.py | Python | gpl-2.0 | 48,332 | [
"FLEUR"
] | 403fdbf5dc75e2157c751aafb055a4caf92f755a249b8a4d735721b3bf788925 |
""" manage PyTables query interface via Expressions """
import ast
import time
import warnings
from functools import partial
from datetime import datetime, timedelta
import numpy as np
import pandas as pd
from pandas.compat import u, string_types, DeepChainMap
from pandas.core.base import StringMixin
import pandas.cor... | pjryan126/solid-start-careers | store/api/zillow/venv/lib/python2.7/site-packages/pandas/computation/pytables.py | Python | gpl-2.0 | 20,253 | [
"VisIt"
] | 4073a53a23cd1197cfd5c0623885ac6997a4455483ba4711ca95fc5c846650c3 |
import numpy as np
from pymatgen.io.vasp.outputs import Vasprun
from pymatgen.io.vasp.inputs import Kpoints, Poscar
from pymatgen.io.vasp.sets import MPNonSCFSet
from pymatgen.electronic_structure.bandstructure import Spin
from os.path import join
class Mass_eff():
'''Calculating effective mass via finite differen... | wayn3/masseff | masseff/calc.py | Python | mit | 6,262 | [
"VASP",
"pymatgen"
] | f3cfe6f090ef52ec456ecd4ce2a281acbda5f4b07d4d0f538db9385299493d38 |
# -*- coding: utf-8 -*-
"""
Regression tests for the Test Client, especially the customized assertions.
"""
from __future__ import unicode_literals
import datetime
import itertools
import os
from django.contrib.auth.models import User
from django.contrib.auth.signals import user_logged_in, user_logged_out
from django... | MikeAmy/django | tests/test_client_regress/tests.py | Python | bsd-3-clause | 68,247 | [
"VisIt"
] | db551e99084cea45d42bd02fe40d092d1ca714466b463e06968e62b3ef4416b7 |
import json
import boto3
from botocore.exceptions import ClientError
import pytest
import sure # noqa
from moto import mock_iam
invalid_policy_document_test_cases = [
{
"document": "This is not a json document",
"error_message": "Syntax errors in policy.",
},
{
"document": {
... | william-richard/moto | tests/test_iam/test_iam_policies.py | Python | apache-2.0 | 51,199 | [
"ADF"
] | e1941180d8fede6ca7938fbae5361909ac3a2009e7644f7fed55270ebaa20af6 |
#!/usr/bin/env python3
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
'''Unit tests for misc.GritNode'''
from __future__ import print_function
import contextlib
import os
import sys
import tempfile
... | chromium/chromium | tools/grit/grit/node/misc_unittest.py | Python | bsd-3-clause | 22,930 | [
"xTB"
] | 2df18135908f962717fbf9aab1d6ff78c21b8f46ab2b951025a6baa81f41cc5f |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2004 Martin Hawlisch
# Copyright (C) 2004-2006, 2008 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2009 Gary Burton
# Copyright (C) 2010 Jakim Friant
#
# This program is free software; you can redistribute it and/o... | pmghalvorsen/gramps_branch | gramps/plugins/export/exportgeneweb.py | Python | gpl-2.0 | 19,711 | [
"Brian"
] | 3a48bb60e56d0802295601ac1e6927aa9e4a8ce90403acb06bb7d524eec17446 |
# 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
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google-research/graph-attribution | graph_attribution/featurization.py | Python | apache-2.0 | 4,483 | [
"RDKit"
] | 7fbc28c896d1f2f859f522b4c442571a28d7c08db5180006423b3e16eea8eaff |
"""
A script that takes the compliance dataset (the released version
of which is at https://github.com/ga4gh/compliance/tree/master/test-data)
and turns it into a directory bundle of binary and JSON files suitable
for use by the reference server.
"""
from __future__ import division
from __future__ import print_function... | srblum/server | scripts/prepare_compliance_data.py | Python | apache-2.0 | 6,553 | [
"pysam"
] | fcf55915e4f993954c7ff5731ae826113feca2e0f3897d4a48a1a1f3acd99cc0 |
#!/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 | modules/phase_field/examples/nucleation/refine.py | Python | lgpl-2.1 | 2,149 | [
"MOOSE",
"VTK"
] | 64068241ede0bab48bb466f7c6470f3760ee03d76bb645a3d5f8eb8c8d62cc5c |
"""
Datatype classes for tracks/track views within galaxy.
"""
import data
import tabular, binascii, logging
from galaxy.datatypes.metadata import MetadataElement
from galaxy.datatypes import metadata
import galaxy.model
from galaxy import util
from galaxy.web import url_for
from sniff import *
from galaxy.util.hash_u... | volpino/Yeps-EURAC | lib/galaxy/datatypes/tracks.py | Python | mit | 1,856 | [
"Galaxy"
] | b67611ffb3fcbd641eecaa663f658a075cd6da4f5d671c354cd5aed620dcd8b7 |
# Copyright 2019 DeepMind Technologies Limited
#
# 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 agr... | deepmind/deepmind-research | hierarchical_probabilistic_unet/model.py | Python | apache-2.0 | 24,398 | [
"Gaussian"
] | 8de1dd2261a2c02d138cabffea8f626f829911710bac8e159fb63e6870f0a069 |
# Hidden Markov Models
#
# Author: Ron Weiss <ronweiss@gmail.com>
# and Shiqiao Du <lucidfrontier.45@gmail.com>
# API changes: Jaques Grobler <jaquesgrobler@gmail.com>
"""
The :mod:`sklearn.hmm` module implements hidden Markov models.
**Warning:** :mod:`sklearn.hmm` is orphaned, undocumented and has known
numerical s... | lucidfrontier45/scikit-learn | sklearn/hmm.py | Python | bsd-3-clause | 45,536 | [
"Gaussian"
] | 468c7bdd3d658322838ae1dc34e930e64e4329893c9ccedb337b5e1602c8d4ce |
# Orca
#
# Copyright 2018 Igalia, S.L.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library is di... | GNOME/orca | src/orca/scripts/apps/smuxi-frontend-gnome/__init__.py | Python | lgpl-2.1 | 795 | [
"ORCA"
] | 990e83d883394022a8851e817efce733c51613969ef0fd4b2c7552617811931e |
# gaussian elimination with scaled pivoting
#
# M. Zingale (2013-02-25)
import numpy
def gaussElim(A, b, returnDet=0):
""" perform gaussian elimination with pivoting, solving A x = b A
is an NxN matrix, x and b are an N-element vectors. Note: A
and b are changed upon exit to be in upper triangula... | bt3gl/Numerical-Methods-for-Physics | others/lin_algebra/gauss.py | Python | apache-2.0 | 3,098 | [
"Gaussian"
] | 1a350423e3dfe85ad58d6a4dac680f84e47b6e2d8ddd75d70e8ef02dae343030 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import warnings
import numpy as np
from math import pi
import unittest
import os
from monty.os.path import which
from pymatgen.analysis.local_env import ValenceIonicRadiusEvaluator, \
VoronoiNN, JmolNN, M... | montoyjh/pymatgen | pymatgen/analysis/tests/test_local_env.py | Python | mit | 50,492 | [
"CRYSTAL",
"Jmol",
"Pybel",
"pymatgen"
] | 39f64dc4930a1537122156dad0933a4addb535ebbc40e844a09de69213e98d43 |
#!/usr/bin/env python
'''
Computing hyperfine coupling tensor
'''
from pyscf import gto, scf, dft
from pyscf.prop import hfc
mol = gto.M(atom='''
C 0 0 0
N 0 0 1.1747
''',
basis='ccpvdz', spin=1, charge=0, verbose=3)
mf = scf.UHF(mol).run()
gobj = hfc.uhf.HFC(mf).set(ve... | gkc1000/pyscf | examples/prop/03-hfc.py | Python | apache-2.0 | 517 | [
"PySCF"
] | cb36d8c10014e6b29dcac70d399e36183c5d0e46d3fef7f498f60b4e86bc1217 |
#!/usr/bin/python
# (c) 2013, Cove Schneider
# (c) 2014, Joshua Conner <joshua.conner@gmail.com>
# (c) 2014, Pavel Antonov <antonov@adwz.ru>
#
# 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... | atplanet/ansible-modules-core | cloud/docker/docker.py | Python | gpl-3.0 | 74,697 | [
"VisIt"
] | 1f06e8a5881fe67e7c74462da9b6a99921673592bc2ea573b91b0ba582f4f5b4 |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
# Copyright 2010-2013 The Orca Team
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/structural_navigation.py | Python | gpl-3.0 | 139,024 | [
"ORCA"
] | 8fd88170f2a8936cc67a00ca1f22c6f9d2d487b7c19f97d493491c167c63662d |
from collections import namedtuple
from collections import deque
import random
import numpy as np
import heapq
class NDPoint(object):
"""
A point in n-dimensional space
"""
def __init__(self, x, idx=None):
self.x = np.array(x)
self.idx = idx
def __repr__(self):
return "NDPoi... | eokeeffe/ImageSimilarity-Python | metric_trees/vp_tree.py | Python | mit | 4,582 | [
"VisIt"
] | acc4755a31c996091ba0227c9e82ca8d59a3435df0a83353c0232b7075471ea6 |
#!/usr/bin/env python
import boto
import imp
import json
import os
import subprocess
import webbrowser
from distutils.spawn import find_executable
from fabric.api import local, prompt, require, settings, task
from fabric.state import env
from glob import glob
from oauth import get_document, get_credentials
from time... | cerealcommas/mashgraphics | fabfile/__init__.py | Python | mit | 10,301 | [
"VisIt"
] | 0c86f8fff1154de6b63802579e6713d13218b2f56d77fbfb7720bbb6b86ee04e |
#!/usr/bin/env python
try:
from setuptools import setup, Extension
except ImportError:
from distutils.core import setup, Extension
setup(
name="twistler",
version="0.1",
description="Controller class extensions for Nevow",
author="Brian Muller",
author_email="bmuller@butterfat.net",
lic... | bmuller/twistler | setup.py | Python | mit | 450 | [
"Brian"
] | d4bf03047f1e235952924c520bfcd76f62ca0d20aaa85a783ab51fe7e45c5b05 |
#!/usr/bin/env python
# File created on 09 Feb 2010
from __future__ import division
__author__ = "Greg Caporaso"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight", "Greg Caporaso", "Kyle Bittinger",
"Jens Reeder", "William Walters", "Jose Carlos Clemente Litran",
... | josenavas/qiime | scripts/pick_otus.py | Python | gpl-2.0 | 53,553 | [
"BLAST"
] | cca2981675752682768b1af9363c72b2c36544ca6ede42887d03160dbbb380e0 |
'''
Created on 2013-05-25
@author: brian
'''
from src.util import Vector2
class Pursue(object):
def __init__(self, actor):
self.actor = actor
self.target = None
def condition(self):
if not self.actor.hostile:
return False
self.target = None
for entity in self.actor.getEnemies():
if sel... | Greymerk/python-rpg | src/ai/task/pursue.py | Python | gpl-3.0 | 1,411 | [
"Brian"
] | 92c0ba513f33ba95d357da2bd04cdaffc99276664f9faea320051c49bc0b4ef1 |
#!/usr/bin/env python
"""
Create a DIRAC MoveReplica request to be executed by the RMS
"""
import os
import time
from hashlib import md5
from DIRAC.Core.Base.Script import Script
def getLFNList(arg):
"""get list of LFNs"""
lfnList = []
if os.path.exists(arg):
lfnList = [line.split()[0] for line i... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_move_replica_request.py | Python | gpl-3.0 | 3,963 | [
"DIRAC"
] | 5afed2da33b146f6de8774d0743ed14452b950cb10f4d2bcdc11e2a2c4eb719d |
import unittest
from nose.tools import (assert_is_not_none, assert_true, assert_raises,
assert_in, assert_equal)
import numpy
from sklearn.base import clone
from sknn.mlp import Classifier as MLPC
from sknn.mlp import Layer as L, Convolution as C
class TestClassifierFunctionality(unittest.Te... | gticket/scikit-neuralnetwork | sknn/tests/test_classifier.py | Python | bsd-3-clause | 4,671 | [
"Gaussian"
] | 0ed1620124e4e19dd1258d51d90c6798ff5ff1e50dc8edabe2749c94483be0bc |
import requests
from datetime import datetime
from django.conf import settings
from django.core.urlresolvers import reverse
from django.contrib.auth.models import User
from django.db import models
from django.db.models.signals import post_save, post_delete
from django.dispatch import receiver
from django.utils.html im... | OpenNews/opennews-source | source/people/models.py | Python | mit | 15,545 | [
"VisIt"
] | 110167ac21c370c793d63749d001ef14ac786c03673a346bf8b4eecb75908983 |
# Script control setup area
# script info
__script__.title = 'KKB Plot and Reduction 16.5.2021'
__script__.version = '2.0'
# 15.6.2017 Allow to reduce the detector range
# 15.6. Throw out points below resolution
# 16.6. Tidy up run time to display in the reduction; tidy up display properties
# 11.7.... | Gumtree/Kookaburra_scripts | Internal/KKB-Plot and Reduction_2021-05-16.py | Python | epl-1.0 | 78,516 | [
"CRYSTAL"
] | 184821466b73c8b627d6af5c5f2284d1b1eb487ad7fcac1a9c0c8298e10e6e61 |
#!/usr/bin/python
#Copyright (c) 2016, Justin R. Klesmith
#All rights reserved.
from __future__ import division
from math import log, sqrt, pow
import argparse, os, random
#Set the author information
__author__ = "Justin R. Klesmith"
__copyright__ = "Copyright 2016, Justin R. Klesmith"
__credits__ = ["Justin R. Kles... | JKlesmith/Bioinformatics | ProcessMSA.py | Python | bsd-3-clause | 4,782 | [
"BLAST"
] | 7e8a6ce78d09b5b991ce73444011161c197b96e59534e37d21f65b5b928af901 |
# coding: utf-8
# Copyright © 2016 Bharadwaj Raju <bharadwaj.raju@keemail.me>
# Contributor: Maksudur Rahman Maateen <ugcoderbd@gmail.com>
# This file is part of TextSuggest.
# TextSuggest is free software.
# Licensed under the GNU General Public License 3
# See included LICENSE file or visit https://www.gnu.org/lic... | maateen/TextSuggestBangla | fonts.py | Python | gpl-3.0 | 1,045 | [
"VisIt"
] | d9d877adf64f1c24dc3c584add11c8fdcf2bc3f067f6c35327a22ace4c3c9918 |
#
# Copyright (c) 2009-2013 Christopher L. Felton
#
# This program 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 later version.
#
# T... | zaqwes8811/micro-apps | matlab_ext/external/fixed_point/fixed_point/_fixbv.py | Python | mit | 20,383 | [
"VisIt"
] | c7111a2d81da5e4219d81a691551df211ba26fca62551829265afa808bce5251 |
# -*- coding: utf-8 -*-
"""
Copyright 2016 Randal S. Olson
This file is part of the TPOT library.
The TPOT library 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 op... | bartleyn/tpot | tpot/tpot.py | Python | gpl-3.0 | 80,525 | [
"Gaussian"
] | b6b97a7d489a2a264347e7cc3acacc53b68cdd4db14098913156c28c72ff348e |
from __future__ import unicode_literals
from django.conf import settings
# When True ThumbnailNode.render can raise errors
THUMBNAIL_DEBUG = False
# Backend
THUMBNAIL_BACKEND = 'sorl.thumbnail.base.ThumbnailBackend'
# Key-value store, ships with:
# sorl.thumbnail.kvstores.cached_db_kvstore.KVStore
# sorl.thumbnail.k... | gregplaysguitar/sorl-thumbnail | sorl/thumbnail/conf/defaults.py | Python | bsd-3-clause | 3,966 | [
"Gaussian"
] | 0cd224cd5cc29ae4565519fd9771f92011e7d8c6975bda899b933af96c8ab643 |
from antlr4 import *
from FoxySheep import FoxySheepVisitor, FoxySheepParser
class FullFormEmitter(FoxySheepVisitor):
"""
This class defines a complete generic visitor for a parse tree produced by FoxySheepParser.
"""
def getFullForm(self, e):
"""
Gets the FullForm of the ParseTree ... | rljacobson/FoxySheep | python_target/FoxySheep/FullFormEmitter.py | Python | bsd-2-clause | 31,378 | [
"VisIt"
] | cb11f86baffb03f354e4d204a6277c7c54d0459ba4e43187ce9694b70ff4f964 |
#
# 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... | apache/incubator-singa | test/python/test_api.py | Python | apache-2.0 | 36,911 | [
"Gaussian"
] | dc66047d3e64cf66b9a0d0396e272033ff8884e8ed21f1c5c50ca8ce204d8b39 |
#!/usr/bin/env python
from ase import *
from gpaw import GPAW
import numpy as np
from gpaw.utilities import equal
from gpaw.mpi import rank, world
import time
magmom = 0.0
ng = 16
nhostswrite = [8]
nhostsread = [8]
tests = []
for nkpt in [4]:
for magmom in [3.0]:
test = 'test: nkpt = %d magmom = %1.1f' ... | qsnake/gpaw | oldtest/parallel-restart.py | Python | gpl-3.0 | 2,901 | [
"ASE",
"GPAW"
] | 3e2e7a2808da5f84782c5449de5dc212e08711e8474c93dae0a0fdc29fc16d2d |
# Overpressure functions of U.S. and Soviet origin.
import numpy as np
from scipy.integrate import quad
from glasstone.utilities import convert_units, ValueOutsideGraphError
# First, some utility functions; these should go in a dedicated file eventually
def scale_range(bomb_yield, ground_range):
return ground_ran... | GOFAI/glasstone | glasstone/overpressure.py | Python | mit | 48,426 | [
"BLAST"
] | a925514041fa41b57de807ae422e6ee37bb37ba02f2af6c9b09da2591a286a00 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the CCX dashboard.
"""
from nose.plugins.attrib import attr
from common.test.acceptance.fixtures.course import CourseFixture
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.lms.ccx_dashboard_page import CoachDashb... | pepeportela/edx-platform | common/test/acceptance/tests/lms/test_ccx.py | Python | agpl-3.0 | 2,227 | [
"VisIt"
] | bc2549a3035dec04f92867dc2205394bf03fda9cb1ac14f970286ceed1ee2f8b |
# 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.
#
"""Find and deal with motifs in biological sequence data.
Representing DNA (or RNA or proteins) in a neural network can be difficult
since input seq... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/NeuralNetwork/Gene/Motif.py | Python | gpl-2.0 | 8,335 | [
"Biopython"
] | d1fe1cbda259077cffcc0317d4a5fd553051d0982210d828d6aa02c2185c5202 |
#!/usr/bin/env python
'''unit testing code for pysam.
Execute in the :file:`tests` directory as it requires the Makefile
and data files located there.
'''
import warnings
import unittest
import os
import re
import glob
import sys
import subprocess
import shutil
import pysam
import pysam.samtools
import pysam.bcftools... | pysam-developers/pysam | tests/samtools_test.py | Python | mit | 14,920 | [
"Bioconda",
"pysam"
] | 7d0968f9291134a27b55381783f4c2c2bedc3bb3b2377f2296968f2e813009d4 |
from __future__ import print_function, division
import random
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 import S
from sympy.core.symbol i... | Shaswat27/sympy | sympy/matrices/dense.py | Python | bsd-3-clause | 44,021 | [
"DIRAC"
] | 52348ced9f803f7c429f4b8539a0c814885f01e4d4f25f4f1a103a2aab80e797 |
r"""
Display cryptocurrency coins.
The site offer various types of data such as name, symbol, price, volume, total
supply, et cetera for a wide range of cryptocurrencies in various currencies.
For more information, visit https://coinmarketcap.com
Configuration parameters:
api_key: specify CoinMarketCap api key (d... | valdur55/py3status | py3status/modules/coin_market.py | Python | bsd-3-clause | 6,433 | [
"VisIt"
] | e65ab31931da965fbb7f610e0469dc3ee792c8692857332b61d412d65532ba3c |
from gpaw.io.array import load_array
N, E = load_array('e6x6.dat', transpose=True)
A = 4.05**2 / 2
Ecoh = 3.34
sigma_emt = (1 - (8 / 12.)**.5) * Ecoh / A
sigma_dft = (N[1:] * E[:-1] - N[:-1] * E[1:]) / (2 * A)
print 'EMT: %4.1f meV/A**2' % (sigma_emt * 1000)
for n, s in zip(N[1:], sigma_dft):
print ' %i %6.1f m... | qsnake/gpaw | doc/exercises/surface/surface_tension.py | Python | gpl-3.0 | 478 | [
"GPAW"
] | 2e1d968b3351e314855b49b23f8997968f203f50d5f2d7bb7e578a6f5ba6c777 |
# coding: utf8
{
'!langcode!': 'nl',
'!langname!': 'Nederlands',
'"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN': '"update" is an optional expression like "field1=\'newvalue\'". You cannot update or delete the results of a JOIN',
'%(nrows)s records foun... | pouyana/teireader | webui/applications/grid/languages/nl.py | Python | mit | 16,825 | [
"Elk"
] | 5ab394db8ef6b000b27cf5bceb086cb0482a2de468e6e2c37ff3f0e31cf01563 |
# Post-processing script generated with paraview
try: paraview.simple
except: from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
poisuille_1_vtk = LegacyVTKReader( FileNames=['poisuille_1.vtk'] )
RenderView1 = GetRenderView()
CellDatatoPointData1 = CellDatatoPointData()
SetActiveSource(po... | EvaBr/CFD-Lab | Backup/FinalProjectPresentation/3D_NS_GivenCPPCode/regression_tests/poisuille.py | Python | mit | 1,246 | [
"ParaView",
"VTK"
] | a37461bdeb53dbb077701f4fc290556d5b0ec11d13c48d9705c73f329a3e2651 |
from django.db import models
from django.forms.models import modelform_factory
from django.db.models.signals import post_delete
from django.core.files.storage import default_storage
from django.contrib.auth.models import User
#import sys
#import vtk
#from vtk import *
class MediaModel(models.Model):
title = models... | minaevmike/praktica | Diplom/mysite/dplm/models.py | Python | gpl-2.0 | 1,528 | [
"VTK"
] | fc347a1d7989c89898e7058910ba3fb8746a470e559d00957365ff92c6a8e840 |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | test/test_formulary_drug_package_response.py | Python | apache-2.0 | 10,137 | [
"VisIt"
] | 9bd97a2aa46df1f700dfeecac8b217a6ae188bd5dc0ac8b1760f75da4849de0d |
# -*- coding: utf-8 -*-
###########################################################################
# Copyright (C) 1998-2010 by authors (see AUTHORS.txt ) #
# #
# This file is part of LuxRays. ... | rbrtribeiro/smalllux3 | samples/smallluxgpu2/blender/render_smallluxgpu.py | Python | gpl-3.0 | 95,826 | [
"Gaussian"
] | 78f3e643245d4166c01ac1cebf197af5d89cd96d35972a7239606c72fc8a207d |
import itertools
import pprint
from floodfill import FloodFill
class Element(object):
'''Basic interface for a particle flow element.
Your class should expose the same attributes
'''
def __init__(self):
self.layer = None
self.linked = []
self.locked = False
self.block_la... | semkiv/heppy_fcc | fastsim/pfalgo/links.py | Python | gpl-3.0 | 3,830 | [
"VisIt"
] | 59d4bb1451596a3ad22e26f656eed844b659e6135d6c52469b32927fcc8b88f4 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
#
# 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 v... | Forage/Gramps | gramps/gen/plug/menu/_note.py | Python | gpl-2.0 | 1,780 | [
"Brian"
] | 012f47782f92cca46d91cf5a2cbc3274ef3fe917a0ecbde10620b8f417997baf |
# -*- coding: utf-8 -*-
"""
modify.py
=========
.. argparse::
:module: modify
:func: create_parser
:prog: modify.py
.. moduleauthor:: Geoff Hutchison <geoffh@pitt.edu>
"""
import argparse
import os
import sys
import random
import math
from skimage import morphology
from scipy import misc, ndimage, fftpac... | LangmuirSim/langmuir | LangmuirPython/ga2d/modify.py | Python | gpl-2.0 | 22,592 | [
"Gaussian"
] | 4b062afe2f2abad4f32d98848fce011399b1c0eeb79bde7b0678bf7fb711b6f5 |
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