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# (C) British Crown Copyright 2010 - 2016, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | zak-k/iris | lib/iris/tests/integration/test_trajectory.py | Python | gpl-3.0 | 11,459 | [
"NetCDF"
] | b12c0207025559b8f7c97ba1deac6412d9d1c1de31db783cf8099bbf769b90a0 |
import h5py
import numpy as np
import matplotlib.pyplot as plt
import cmath as m
from scipy import signal
import pylab
from myClasses import fft
matplotlib.rcParams.update( {'font.size':22})
ft = fft()
f = h5py.File("/home/flb41892/data/Nexus different parameters/NLC on Res8 ZF4 HFL 7899 PR16.0.nxs","r")
s = f["entr... | DiamondLightSource/FTIR-Filtering-Experimental | 2 Class FFT (filter and no filter)/src/ft_Opus_Equivalent.py | Python | apache-2.0 | 9,914 | [
"Gaussian"
] | dc5d99218db369023e617cea301ee7074358623c595f705e2b9cc6ee223e7dec |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/core/ui/exceptionform.py | Python | gpl-2.0 | 9,892 | [
"Brian"
] | 86fb118999b8b7be21943be08c1b9c57b08ec8f690a69cbefbfabea591b2de56 |
# Copyright (c) 2003-2010 Sylvain Thenault (thenault@gmail.com).
# Copyright (c) 2003-2010 LOGILAB S.A. (Paris, FRANCE).
# 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 L... | isohybrid/dotfile | vim/bundle/git:--github.com-klen-python-mode/pylibs/pylint/checkers/format.py | Python | bsd-2-clause | 14,407 | [
"VisIt"
] | d846ea4273b4252f8a594aa938fd0f7f718d79bfed9a1049c04c7c86d1a37b10 |
from skidl import SKIDL, TEMPLATE, Part, Pin, SchLib
SKIDL_lib_version = '0.0.1'
maxim = SchLib(tool=SKIDL).add_parts(*[
Part(name='DS1267_DIP',dest=TEMPLATE,tool=SKIDL,keywords='Dual Digital Potentiometer Maxim',description='Dual Digital Potentiometer, Serial, 256 Steps, DIP-14',ref_prefix='U',num_units=1,fp... | xesscorp/skidl | skidl/libs/maxim_sklib.py | Python | mit | 14,100 | [
"CRYSTAL"
] | 1612b254e23023779ccacb10027ccc1f3c81e2e6b51f7cf14904998c6ea73470 |
import warnings
import numpy as np
from ._felzenszwalb_cy import _felzenszwalb_grey
def felzenszwalb(image, scale=1, sigma=0.8, min_size=20):
"""Computes Felsenszwalb's efficient graph based image segmentation.
Produces an oversegmentation of a multichannel (i.e. RGB) image
using a fast, minimum spannin... | emmanuelle/scikits.image | skimage/segmentation/_felzenszwalb.py | Python | bsd-3-clause | 3,030 | [
"Gaussian"
] | 6391f6c8e36e397b4ad1c4dcda5096784d00e8f8d245c51dc4bced6f10e61631 |
# Author: Prabhu Ramachandran
# Copyright (c) 2004, Enthought, Inc.
# License: BSD Style.
"""This module generates the class hierarchy for any given Python
modules. This can be used (among other things) to generate the
traitified VTK classes in the correct order.
"""
import __builtin__
class TreeNode... | VisTrails/vistrails-contrib-legacy | vtksnl/class_tree.py | Python | bsd-3-clause | 8,340 | [
"VTK"
] | 3959e5ffbaa89708722ebc116f973c41795540d74e5d3db17830d33a6117018a |
r"""
Ordination methods (:mod:`skbio.stats.ordination`)
==================================================
.. currentmodule:: skbio.stats.ordination
This module contains several ordination methods, including Principal
Coordinate Analysis, Correspondence Analysis, Redundancy Analysis and
Canonical Correspondence Analy... | SamStudio8/scikit-bio | skbio/stats/ordination/__init__.py | Python | bsd-3-clause | 3,919 | [
"scikit-bio"
] | 6420683837aa20a64a0a0f68a40b698362e8ec33025bfb4a071538a932e398f8 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | kdmurray91/scikit-bio | skbio/stats/ordination/tests/test_redundancy_analysis.py | Python | bsd-3-clause | 6,579 | [
"scikit-bio"
] | 9ae2d1d9ea1b9eb5f6d03e984caa0f82a801f8cb08468f1fb414bd8ac2c53152 |
# -*- coding: UTF-8 -*-
__revision__ = '$Id$'
# Copyright (c) 2005-2011 Vasco Nunes, Piotr Ożarowski
#
# 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... | marcin1j/griffith | lib/plugins/movie/PluginMovieCineMovies.py | Python | gpl-2.0 | 10,036 | [
"CRYSTAL"
] | f53685c88154f3c5d7f2363a470437a0273b364ccfc3d5c4d6b2c1fb78aac6fb |
#!/usr/bin/env python
"""
Get information on resources available for the given VO: Computing and Storage.
By default, resources for the VO corresponding to the current user identity are displayed
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ ... | ic-hep/DIRAC | src/DIRAC/Resources/scripts/dirac_resource_info.py | Python | gpl-3.0 | 5,120 | [
"DIRAC"
] | ad484f1bcc4f96c3e77d27cf211febcbba6b528fa8bc55c562d6b29b4373eb6f |
#! /usr/bin/env python
"""
Calculate the rotational constants of a molecule.
Reads Turbomole format coord files and returns the three rotational
constants of the system specified therein. Can take multiple coord
files as argument.
@author Matt Agee
"""
import numpy as np
import sys
import argparse
class KnownErro... | magee256/TurbomoleScripts | OutputParsing/Production/get_rot_const/get_rot_const.py | Python | mit | 7,409 | [
"TURBOMOLE"
] | a1a130dcfd7df058bff3091b0507faec91a614de5616235b3925f76ed314b335 |
# $Id$
#
# Copyright (C) 2000-2006 greg Landrum and Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
""" a set of function... | ptosco/rdkit | rdkit/Dbase/DbUtils.py | Python | bsd-3-clause | 14,536 | [
"RDKit"
] | c9c5422cc3937b8be2c1026b1d32f4974c14208d7ecf4131a5986da93df48f70 |
"""
Tests for nwchem package.
"""
| materialsproject/custodian | custodian/nwchem/tests/__init__.py | Python | mit | 34 | [
"NWChem"
] | d04189eb3c92b8e0051f60cb0d86b0a9b0a4c9d08153e2e7061a736559193c3d |
###############################################################################
##
## Copyright (C) 2014-2016, New York University.
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## ... | VisTrails/VisTrails | vistrails/gui/application_server.py | Python | bsd-3-clause | 108,131 | [
"VTK",
"VisIt"
] | 4d5f2b724bab51247401613f3c895d5871a7c41d7f87e3d9cd9e085369caf37d |
import numpy as np
import scipy.interpolate
import matplotlib.pyplot as plt
np.random.seed(1977)
x, y, z = np.random.random((3, 10))
yi, xi = np.mgrid[0:1:100j, 0:1:100j]
interp_types = ['multiquadric', 'inverse', 'gaussian', 'linear', 'cubic',
'quintic', 'thin_plate']
for kind in interp_types:
i... | igryski/TRMM_blend | src/blend/thin_plate_spline_comparison.py | Python | gpl-3.0 | 609 | [
"Gaussian"
] | 38851401290017c12ddf7a95577d48e876ea1541a5fa408a9ab221a07cc76d9d |
'''
PyPDB: A Python API for the RCSB Protein Data Bank
-----
GitHub: https://github.com/williamgilpin/pypdb
PyPI: https://pypi.python.org/pypi/pypdb
-----
If you find this code useful, please consider citing the paper:
Gilpin, W. "PyPDB: A Python API for the Protein Data Bank."
Bioinformatics, Oxford Jour... | williamgilpin/pypdb | pypdb/pypdb.py | Python | mit | 33,995 | [
"BLAST",
"CRYSTAL"
] | bec729ed2fb61874d648c62270890787dcdaaf6f64d550854bb8be947b1ee749 |
#
# Copyright (C) 2007, Mark Lee
#
# http://rl-glue-ext.googlecode.com/
#
# 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 require... | evenmarbles/rlglued | rlglued/environment/loaderscript.py | Python | bsd-3-clause | 1,668 | [
"Brian"
] | 08ab44e303e989ce8d79dec3335de7044aa42b1e44c745e0f282c819f9eb5d3d |
# -*- coding: utf-8 -*-
#
# test_regression_issue-1034.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 ... | sanjayankur31/nest-simulator | testsuite/pytests/test_regression_issue-1034.py | Python | gpl-2.0 | 13,015 | [
"NEURON"
] | 8c51bed68648ab265de29900c620db81bc91c8951527f8b6a9f10c1407234487 |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/mooseutils/ImageDiffer.py | Python | lgpl-2.1 | 6,141 | [
"MOOSE"
] | df6c1ee2952fe1ce02a6d9dad1fd1a9e8e793ce4f9fe137a6788519f1a03dfc2 |
# Copyright Emin Martinian 2002. See below for license terms.
# Version Control Info: $Id: genericmatrix.py,v 1.4 2003/10/28 21:42:56 emin Exp $
"""
This package implements the GenericMatrix class to provide matrix
operations for any type that supports the multiply, add, subtract,
and divide operators. For example,... | jpahullo/python-multiprocessing | py_ecc/genericmatrix.py | Python | gpl-3.0 | 30,777 | [
"Gaussian"
] | 3a97b6ff4f6a9b789c3e45b84b8bf12532182f79f96a8a7e46766daf4c0e77fe |
"""
@name: /home/briank/workspace/PyHouse_Install/src/Install/wifi.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2016-2016 by D. Brian Kimmel
@license: MIT License
@note: Created Feb 4, 2016
@Summary: Fix the WiFi adapter
On Raspis the wireless adapter sometimes goes ... | DBrianKimmel/PyHouse_Install | src/Install/wifi.py | Python | mit | 1,209 | [
"Brian"
] | d2c4fb384dc06c277860fb2b5f04b4d8e9b66a074ab07dd9be138fcf5599df8f |
"""
Unit tests for the stem.util.enum class and functions.
"""
import unittest
import stem.util.enum
class TestEnum(unittest.TestCase):
def test_enum_examples(self):
"""
Checks that the pydoc examples are accurate.
"""
insects = stem.util.enum.Enum('ANT', 'WASP', 'LADYBUG', 'FIREFLY')
self.as... | DigiThinkIT/stem | test/unit/util/enum.py | Python | lgpl-3.0 | 1,441 | [
"Firefly"
] | 506b87f53375080fdde28b461fa3db4b796ced56e9abdc093cc7e20a48b28d87 |
# This file is part of the myhdl library, a Python package for using
# Python as a Hardware Description Language.
#
# Copyright (C) 2003-2015 Jan Decaluwe
#
# The myhdl 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 t... | j-marjanovic/myhdl | myhdl/_intbv.py | Python | lgpl-2.1 | 15,992 | [
"VisIt"
] | 7fc64d55db5b71581eef236a27a47dcfcc7bd55e29554447638bc3457d662883 |
# -*- coding: utf-8 -*-
#
# Copyright © 2013-2017 Michael Rabbitt, Roberto Alsina and others.
#
# 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 limita... | xuhdev/nikola | nikola/plugins/compile/markdown/mdx_podcast.py | Python | mit | 3,641 | [
"Brian"
] | 2f8e1f9a060d960a1b57090b9ea49d12709fc909b33496d9a160014a5f4030c5 |
from Lexer import Lexer
from Parser import Parser
from NodeVisitor import NodeVisitor
from Constants import *
class Infix2Language(NodeVisitor):
def __init__(self, tree):
self.tree = tree
self.language = {
PLUS: "plus",
MINUS: "minus",
MUL: "times",
DIV: "div"
}
def visit_BinOp(self, node):
left... | Zephyrrus/ubb | YEAR 3/SEM 2/DP/Lab2/main.py | Python | mit | 929 | [
"VisIt"
] | 36a1e2673432ed129bbdaa084dbb5c789d83b2389f063f3eb6beaf6c6768ca97 |
# -*- coding: utf-8 -*-
"""
(c) 2019 - Copyright Red Hat Inc
Authors:
Pierre-Yves Chibon <pingou@pingoured.fr>
"""
from __future__ import unicode_literals, absolute_import
import arrow
import copy
import datetime
import unittest
import shutil
import sys
import time
import os
import flask
import json
import m... | pypingou/pagure | tests/test_pagure_flask_api_project_blockuser.py | Python | gpl-2.0 | 8,717 | [
"VisIt"
] | 6350d4dd0dd8c666349e632e7b1b2cf83f086abbd1d0e7a2795b9648bdf968e3 |
# Tilt and orientation factor
#
# Ladybug: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Ladybug.
#
# Copyright (c) 2013-2015, Djordje Spasic <djordjedspasic@gmail.com>
# Ladybug is free software; you can redistribute it and/or modify
# it under the term... | boris-p/ladybug | src/Ladybug_Tilt And Orientation Factor.py | Python | gpl-3.0 | 48,184 | [
"EPW"
] | a033ff5ac79d0489f129a537f52c51570f18187639319193e2fac483c90f91f3 |
#!/usr/bin/env python
"""
Training and using a KNN for 1D data interpolation and extrapolation.
Comparison of training methods, EKF vs SGD.
"""
# Dependencies
from __future__ import division
import numpy as np
import matplotlib.pyplot as plt
import kalmann
# Get some noisy training data, a fun compact function
stdev ... | jnez71/kalmaNN | demos/1d_fit.py | Python | mit | 1,201 | [
"NEURON"
] | 67534581f63f5153e438a769919281673a52e27eb0ae491b6272b8c86775cee6 |
# Copyright (C) 2014
# Pierre de Buyl
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it ... | govarguz/espressopp | src/interaction/HarmonicTrap.py | Python | gpl-3.0 | 2,990 | [
"ESPResSo"
] | 4c1736b4fc1b85083eb973bff6a48773d9ae55fad1431da12b0bf49fb020d7c0 |
########################################################################
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/07/19 12:16:39
########################################################################
""" :mod: TypedListTests
=======================
.. module: TypedListTests
:synopsis: tes... | andresailer/DIRAC | Core/Utilities/test/Test_TypedList.py | Python | gpl-3.0 | 2,941 | [
"DIRAC"
] | dbabafc165502d0141feca831981bbc0d760e824c07d00b30589df18e81fa1b2 |
import os
import numpy as np
#numpy.seterr(all='raise')
from ase import Atom
from ase.io.plt import write_plt
from gpaw.test import equal
from gpaw import GPAW
from gpaw.cluster import Cluster
from gpaw.io.plt import read_plt
txt='-'
txt='/dev/null'
load = False
#load = True
R=0.7 # approx. experimental bond length... | qsnake/gpaw | gpaw/test/plt.py | Python | gpl-3.0 | 1,364 | [
"ASE",
"GPAW"
] | 1bb0d3f03a2ba44ef42fd33b87582e092bcee713a00f742eb542d644586cedd5 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module defines classes to represent any type of spectrum, essentially any
x y value pairs.
"""
from typing import List
import numpy as np
from monty.json import MSONable
from scipy.ndimage.filters im... | davidwaroquiers/pymatgen | pymatgen/core/spectrum.py | Python | mit | 6,493 | [
"Gaussian",
"pymatgen"
] | cfa9d23f5d68b813f2168862c6ea0dd27a5e85ce2022994acd9ba448dc5ccee6 |
"""
Module containing a NeuroML2 cell class
"""
from __future__ import unicode_literals
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
from future import standard_library
standard_library.install_aliases()
from copy import deepcopy
from neuron import h # ... | Neurosim-lab/netpyne | netpyne/cell/NML2Cell.py | Python | mit | 844 | [
"NEURON"
] | 666e5fe48858cf6675ff1b4aefa4e775fab8c3ea965b8133705d1605f8fb7420 |
import sys, os, glob, string
import numpy as np
import astropy as ast
import matplotlib.pyplot as plt
from pyraf import iraf
import odi_config as odi
import pandas as pd
from astropy.coordinates import SkyCoord
from astropy import units as u
from collections import OrderedDict
def tpv_remove(img):
"""
Remove t... | bjanesh/odi-tools | full_calibrate.py | Python | bsd-3-clause | 47,754 | [
"Gaussian"
] | cf83b72a9ecb44e6406944cda97f087a16b28beb2745d5db4574aff18c5f271c |
"""
Trace options
-------------
This feature is currently in development...
The trace options settings allow you to track the movement of the visible
atoms within the filter list. This will calculate the displacement of all
visible atoms and draw a tube/bond from their initial locations to their
current positions.... | chrisdjscott/Atoman | atoman/gui/filterListOptions/traceOptions.py | Python | mit | 5,472 | [
"VTK"
] | b742bbd3b4e2a1940ce9a4cfb8c106dee511cc673eb95a6706934b2036bee821 |
#
# 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
import time
m = 1000
n = 2000
testMehrotra = ... | sg0/Elemental | examples/interface/LPDirectDense.py | Python | bsd-3-clause | 3,301 | [
"Gaussian"
] | 4bb8b9aa792ba52f45f248d4a83bc3f6dc18044d5ff523410c465547a8c8ac97 |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | smu/generate_properties_table.py | Python | apache-2.0 | 7,078 | [
"ORCA",
"RDKit",
"TURBOMOLE"
] | e34d2b4ffecb475bffbce43855703f3e720f3d70c1435d402e09aeb17b76e525 |
# Created By: Omar Quazi
# Copyleft 2014 under the GNU GPL v3. You are permitted to redistribute
# this program with or without modifications; but, the copy must retain this
# license agreement.
# For the full license, please visit the Free Software Foundation:
# https://www.gnu.org/copyleft/gpl.html
from getpass imp... | blacksector/FolderLockWin | main.py | Python | gpl-3.0 | 2,252 | [
"VisIt"
] | f2f1f4eea96c8032d9502b06351ac5cdb9bf36730639ac2611a9a33ca04781e3 |
# -*- coding: utf-8 -*-
"""
This modules provides functions to calculate correlations between spike trains.
:copyright: Copyright 2015-2016 by the Elephant team, see `doc/authors.rst`.
:license: Modified BSD, see LICENSE.txt for details.
"""
from __future__ import division, print_function, unicode_literals
import war... | apdavison/elephant | elephant/spike_train_correlation.py | Python | bsd-3-clause | 38,205 | [
"DIRAC",
"NEURON"
] | 9a51302f6a02b8a5e76f26065721831f5faffd062c2be224ecf46fa2e1c358e7 |
#!/usr/bin/env python
"""
Abstract: Iterate through all folders and perform adapter trimming on all
reads. This script uses a sequencing mapping file to map wells to
sampleids and trim 5'-end adapters of reads. Additionally, reads with
lengths <200 nt are discarded. For more information o... | akshayparopkari/kadambari | python/trim_five_prime_end_adapters.py | Python | bsd-3-clause | 10,958 | [
"VisIt"
] | 4fe03dda820a3c2cefb8b23f2db7ffe2cf4de7de1136ce89c4eaef0fa6a5ea15 |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import gtk
import os
from zeroinstall.gtkui import gtkutils
last_error = None
builderfile = os.path.join(os.path.dirname(__file__), 'zero-install.ui')
class Template(gtkutils.Template):
def __init__(self, root):
... | dabrahams/zeroinstall | zeroinstall/0launch-gui/dialog.py | Python | lgpl-2.1 | 1,043 | [
"VisIt"
] | 911378edacb48a1add4501aa672b449ae7e7ef043fc2a8bdee05fc8c0c96d55e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# PyGoo - An Object-Graph mapper
# Copyright (c) 2010 Nicolas Wack <wackou@gmail.com>
#
# PyGoo 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 ... | wackou/pygoo | tests/test_datamodel.py | Python | gpl-3.0 | 15,809 | [
"GULP"
] | 93bb6c3009f6dedf0ce4be128484e1df8b1d165e07974f571b1aba789d970aca |
"""
==================
Two-class AdaBoost
==================
This example fits an AdaBoosted decision stump on a non-linearly separable
classification dataset composed of two "Gaussian quantiles" clusters
(see :func:`sklearn.datasets.make_gaussian_quantiles`) and plots the decision
boundary and decision scores. The di... | RPGOne/Skynet | scikit-learn-c604ac39ad0e5b066d964df3e8f31ba7ebda1e0e/examples/ensemble/plot_adaboost_twoclass.py | Python | bsd-3-clause | 3,199 | [
"Gaussian"
] | e195f09d055e38bd498e9b1a2444fec783cc0afe8e7058c63d3ac7989eed1ed4 |
# Copyright 2015 Kevin B Jacobs
#
# 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... | bioinformed/vgraph | vgraph/bed.py | Python | apache-2.0 | 4,566 | [
"pysam"
] | 20e5eba9e61649e7b5e9653627c5774b109336d4fe99e56ba89def332c166af7 |
""" Class for handling several simultaneous jobs.
The class has been tested on Niflheim-opteron4.
"""
from multiprocessing import Pool
import time
from ase.io import write, read
class MultiprocessingRun(object):
"""Class that allows for the simultaneous relaxation of
several candidates on a cluster. Best used... | suttond/MODOI | ase/ga/multiprocessingrun.py | Python | lgpl-3.0 | 1,938 | [
"ASE"
] | f8aa54819bfb6a2ba66e1291952641c5f668cbedb4ffe1e96fc4d961f9027525 |
#! /usr/bin/env python
"""
Module with functions for correcting bad pixels in cubes.
"""
__author__ = 'Carlos Alberto Gomez Gonzalez, V. Christiaens'
__all__ = ['frame_fix_badpix_isolated',
'cube_fix_badpix_isolated',
'cube_fix_badpix_annuli',
'cube_fix_badpix_clump']
import numpy ... | carlgogo/vip_exoplanets | vip_hci/preproc/badpixremoval.py | Python | bsd-3-clause | 46,363 | [
"Gaussian"
] | fcb26ac3333f18dbebf59a18eb96c803da38e4fea736eaad0bf389cfb6d02046 |
from ase import Atom, Atoms
from gpaw import GPAW
from gpaw.test import equal
a = 4.05
d = a / 2**0.5
bulk = Atoms([Atom('Al', (0, 0, 0)),
Atom('Al', (0.5, 0.5, 0.5))],
pbc=True)
bulk.set_cell((d, d, a), scale_atoms=True)
h = 0.25
calc = GPAW(h=h,
nbands=2*8,
... | robwarm/gpaw-symm | gpaw/test/cg.py | Python | gpl-3.0 | 897 | [
"ASE",
"GPAW"
] | 5d5794956361d9b583f7a8869afe27da248c363512cde5d63549df9707437341 |
#import superimport
import os
import matplotlib.pyplot as plt
import numpy as np
from numpy import linalg
from mpl_toolkits.mplot3d import Axes3D
from inspect import getsourcefile
from os.path import abspath
#https://stackoverflow.com/questions/2632199/how-do-i-get-the-path-of-the-current-executed-file-in-python?l... | probml/pyprobml | scripts/pyprobml_utils.py | Python | mit | 5,646 | [
"Gaussian"
] | d9ca7fdfd71cefae67f47f5c1066f7a1a760fd70362054fc29e1b330f492c84c |
import pysam
import os
import gzip
import numpy as np
import struct
from stat import S_ISREG
from .vcf_record import VaseRecord
from .vcf_header import VcfHeader
from .utils import reg2bins
MAX_INT32 = int(2**31 - 1)
class VcfReader(object):
'''
A class providing some parsing niceties for working with VC... | gantzgraf/vape | vase/vcf_reader.py | Python | gpl-3.0 | 13,270 | [
"pysam"
] | d282d9315392e2901e2a18675c0dcc22e5b0c3d77127872581d78f262e78b50e |
from .models import Activity
from .models import Visit
from datetime import datetime, date
from django.db.models import Count
from django.conf import settings
from django.core.mail import EmailMessage
from django.template.loader import render_to_string
from smtplib import SMTPException
from common.notify import Notify
... | linea-it/dri | api/activity_statistic/reports.py | Python | gpl-3.0 | 8,235 | [
"VisIt"
] | e45f84a9ef70b645d87191b10f557ca14078d9517cdbcbeb02f3cbb5569df965 |
"""
Loadable.Loadable subclass
"""
# This file is part of Munin.
# Munin is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
# Munin is ... | munin/munin | munin/mod/status.py | Python | gpl-2.0 | 11,889 | [
"Galaxy"
] | 5dabdce0239e04587317d1a61d6a0f7e5fcc434f5b754fa06e91390fdbfa5261 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove ... | gratefulfrog/lib | python/chempy/solvate.py | Python | gpl-2.0 | 2,043 | [
"ChemPy",
"PyMOL"
] | e29c12aced49f15b28585d2b9dd9ab394691c145587e5ca65606e3ddc853973c |
#emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
#ex: set sts=4 ts=4 sw=4 et:
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
# See the COPYING file distributed along with the smile package for the
# copyright and license terms.
#
### ### ### ### ### ### ### ... | ischleifer/smile | smile/state.py | Python | gpl-3.0 | 32,826 | [
"Octopus"
] | 60bdb02414fef7fee6faec5327a73a9298de0a0499c5027e93b85cc2aaef5ab8 |
import numpy as np
def disp_in_box(drij, box):
""" Enforce minimum image convention (MIC) on displacement vectors.
Args:
drij (np.array): ri - rj for all pairs of particles rij
box (np.array): side lengths of orthombic box
Return:
np.array: displacement vectors under MIC.
"""
ndim = drij.shape[-... | Paul-St-Young/solid_hydrogen | qharv_db/grsk.py | Python | mit | 9,425 | [
"ASE"
] | 829c7a2057f65f1f842670f36b85ea80b66d6f347c063787dc926ace734cad89 |
r"""*Module for* ``sphobjinv`` *CLI* |Inventory| *writing*.
``sphobjinv`` is a toolkit for manipulation and inspection of
Sphinx |objects.inv| files.
**Author**
Brian Skinn (bskinn@alum.mit.edu)
**File Created**
19 Nov 2020
**Copyright**
\(c) Brian Skinn 2016-2022
**Source Repository**
https://gith... | bskinn/sphobjinv | src/sphobjinv/cli/write.py | Python | mit | 7,234 | [
"Brian"
] | 55ded2c48a98c848cf04ba9c53f9a28ba291532c5c59c67eaf71afb669510fb9 |
__author__ = 'junz'
import numpy as np
import os
import scipy.ndimage as ni
import scipy.sparse as sparse
import math
import matplotlib.pyplot as plt
from itertools import combinations
from operator import itemgetter
import skimage.morphology as sm
import skimage.transform as tsfm
import cv2
import matplotlib.colors a... | zhuangjun1981/retinotopic_mapping | retinotopic_mapping/RetinotopicMapping.py | Python | gpl-3.0 | 111,703 | [
"Gaussian"
] | b4ce297cc189307843cc0b0c366e3c532cef074eb648723fbc4a5302b99d4733 |
# -*- coding: utf-8 -*-
import math
from chempy.chemistry import Reaction
from chempy.util.testing import requires
from chempy.units import units_library, allclose, default_units as u
from ..arrhenius import arrhenius_equation, ArrheniusParam, ArrheniusParamWithUnits
def test_arrhenius_equation():
assert abs(... | bjodah/aqchem | chempy/kinetics/tests/test_arrhenius.py | Python | bsd-2-clause | 1,612 | [
"ChemPy"
] | cfc63af7e52166497817ef2f2fc66fe7353e05f507e1f627efbe7e9018bf38da |
"""
A buffered iterator for big arrays.
This module solves the problem of iterating over a big file-based array
without having to read it into memory. The `Arrayterator` class wraps
an array object, and when iterated it will return sub-arrays with at most
a user-specified number of elements.
"""
from __future__ impo... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/numpy/lib/arrayterator.py | Python | agpl-3.0 | 7,244 | [
"NetCDF"
] | fb382e548b901eb746665c63bfe01cc92b5a9571970ee18385747e70324918df |
#!C:\OSGEO4~1\bin\python.exe
# ******************************************************************************
# $Id: rgb2pct.py 8e263710cb425c4a8b76b1f363b98be41ea0a983 2018-04-30 19:40:20 +1000 Ben Elliston $
#
# Name: rgb2pct
# Project: GDAL Python Interface
# Purpose: Application for converting an RG... | kubaszostak/gdal-dragndrop | osgeo/apps/Python27/Scripts/rgb2pct.py | Python | mit | 7,098 | [
"NetCDF"
] | 5b0ca92f997ed9248c1cac0bf6744b43a9382549865b41f3a39e18cd19634c0f |
"""
The goal of this challenge is to create a function that will take a list of
names and a bin size and then shuffle those names and return them in a
list of lists where the length of the inner lists matches the bin size.
For example calling the function with a list of names and the size of 2 should return
a lis... | developerQuinnZ/this_will_work | student-work/Nathan_Burchfield/week_1/group_challenge/names_challenge.py | Python | mit | 1,270 | [
"Elk"
] | 4b3c6422ca3f2e7e91b11ff0ab7a61703bbf9bbadf385da2c7e0e51ece202d3a |
# Copyright: (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
# Copyright: (c) 2016, Toshio Kuratomi <tkuratomi@ansible.com>
# Copyright: (c) 2018, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# Make coding more python3-ish
from __future__ import ... | Dhivyap/ansible | lib/ansible/cli/__init__.py | Python | gpl-3.0 | 20,402 | [
"Galaxy"
] | 3d6574fc24238268c8e6a46e355874d6eacce4cc3da526480a045f4dc69da90a |
"""Next gen sequence alignments with Bowtie2.
http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
"""
import os
from bcbio.pipeline import config_utils
from bcbio.distributed.transaction import file_transaction
from bcbio.provenance import do
from bcbio import bam, utils
from bcbio.pipeline import datadict as dd
fr... | brainstorm/bcbio-nextgen | bcbio/ngsalign/bowtie2.py | Python | mit | 6,551 | [
"Bowtie",
"Galaxy"
] | 9a9316f8da23280afd3ce99c1e6d647b4e6ce1d06a263a2ece013fdd964e8c46 |
"""Tests for the CheckMigration Operation"""
import functools
import pytest
from mock import MagicMock
from DIRAC import S_OK
from DIRAC.RequestManagementSystem.Client.File import File
from DIRAC.RequestManagementSystem.Client.Operation import Operation
from DIRAC.RequestManagementSystem.Client.Request import Reques... | fstagni/DIRAC | DataManagementSystem/Agent/RequestOperations/test/Test_CheckMigration.py | Python | gpl-3.0 | 4,100 | [
"DIRAC"
] | bd8266a2a92f4690eb496206ca12b65d9a354084ed4283bad8e78a0c11ee4381 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source
##
## 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 2
## of the License, or ... | andrebellafronte/stoq | stoqlib/reporting/report.py | Python | gpl-2.0 | 10,857 | [
"VisIt"
] | 1936e19d5bf59e912b96da450e5aba43fa765fce933b54d96fda824de296cd80 |
"""
[2016-01-04] Challenge #248 [Easy] Draw Me Like One Of Your Bitmaps
https://www.reddit.com/r/dailyprogrammer/comments/3zfajl/20160104_challenge_248_easy_draw_me_like_one_of/
Let's build a basic paint program! Your task for today will be to create a basic paint program that can draw points,
lines, and filled recta... | DayGitH/Python-Challenges | DailyProgrammer/DP20160104A.py | Python | mit | 5,353 | [
"exciting"
] | 432a67be71df5cc62c9608fc2c5b156bad54d083bc737740355376b3fdd36d60 |
"""Module for RBF interpolation."""
import warnings
from itertools import combinations_with_replacement
import numpy as np
from numpy.linalg import LinAlgError
from scipy.spatial import KDTree
from scipy.special import comb
from scipy.linalg.lapack import dgesv # type: ignore[attr-defined]
from ._rbfinterp_pythran i... | e-q/scipy | scipy/interpolate/_rbfinterp.py | Python | bsd-3-clause | 16,523 | [
"Gaussian"
] | 0a45ef40568def6bb5995cd3bdc5202199782d819b5e4c406e9f6942ce804a8a |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | tensorflow/tensorflow | tensorflow/python/ops/nn_ops.py | Python | apache-2.0 | 262,886 | [
"Gaussian"
] | 93cbc6423134902c32438c3c52f91efc8f0b40d820222271420140cad9aa085e |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2018, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Universe Notebook Widget
#########################
To visualize a universe containing atoms, molecules, orbitals, etc., do
the following in a Jupyter notebook environment.
.. co... | alexvmarch/atomic | exatomic/widgets/widget.py | Python | apache-2.0 | 24,119 | [
"ADF",
"Gaussian"
] | 02194421625cefb7ff9519a8450821a251a99a4a5d157f0fb56ecd703f2927d6 |
import morb
from morb import rbms, stats, updaters, trainers, monitors
import theano
import theano.tensor as T
import numpy as np
import gzip, cPickle
import matplotlib.pyplot as plt
plt.ion()
from utils import generate_data, get_context
# DEBUGGING
from theano import ProfileMode
# mode = theano.ProfileMode(opti... | benanne/morb | examples/example_mnist_persistent.py | Python | gpl-3.0 | 4,886 | [
"Gaussian"
] | 86c8cb84adeb8de22b64b57013e8a3368b7078c28f24ed66b6b071b3f2b17624 |
#######################################################################
#
# Inputmod for VU+ by markusw and schomi (c) 2013
# www.vuplus-support.org
#
# This plugin is licensed under the Creative Commons
# Attribution-NonCommercial-ShareAlike 3.0 Unported License.
# To view a copy of this license, visit http://creative... | popazerty/e2-gui | lib/python/Plugins/Extensions/FilebrowserVTi/Inputmod.py | Python | gpl-2.0 | 7,581 | [
"VisIt"
] | 1cf873178d3e40567304498918acbbbae739ba6e1ab1713e0df91c9616a32ae4 |
#!/usr/bin/env python
__author__ = "waroquiers"
from pymatgen.analysis.chemenv.connectivity.connectivity_finder import (
ConnectivityFinder,
)
from pymatgen.analysis.chemenv.connectivity.structure_connectivity import (
StructureConnectivity,
)
from pymatgen.analysis.chemenv.coordination_environments.chemenv_... | davidwaroquiers/pymatgen | pymatgen/analysis/chemenv/connectivity/tests/test_structure_connectivity.py | Python | mit | 2,416 | [
"pymatgen"
] | 85e350f5a0fadcdf0ddd88c0092fa0db0c4f25f6c79d2fb78094e3cc4dfa48f3 |
import traceback
from asyncio import gather, Lock, Semaphore, sleep, CancelledError
from collections import deque
from time import time, monotonic
from queue import Empty, Full
from itertools import cycle
from sys import exit
from math import ceil
from distutils.version import StrictVersion
from functools import lru_ca... | DavisPoGo/Monocle | monocle/worker.py | Python | mit | 83,030 | [
"VisIt"
] | 8d83067ffaeb3ef44521c8ec7d334276d33441b893535651c5a5708f6241815a |
"""Stateful programmatic WWW navigation, after Perl's WWW::Mechanize.
Copyright 2003-2006 John J. Lee <jjl@pobox.com>
Copyright 2003 Andy Lester (original Perl code)
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD or ZPL 2.1 licenses (see the file COPYING.txt
included w... | Masood-M/yalih | mechanize/_mechanize.py | Python | apache-2.0 | 31,059 | [
"VisIt"
] | ae63fa1287a53d0af385cfdf3a95db47c9498e8d2db3e96c0c6811a09f75d225 |
# -*- coding: utf-8 -*-
"""
Output Plugin for F-IIS MP3S Encoder.
Copyright (c) 2006-2008 by Nyaochi
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 ... | rinrinne/cueproc-alternative | src/ce_fiismp3.py | Python | gpl-2.0 | 2,896 | [
"VisIt"
] | b0c41ececa0ab0ed236361ee51ad43a7552f03d19dd50401a12c75cdc2ab07de |
import pytest
from .facebook import FacebookProvider
from .github import GithubProvider
from .google import GoogleProvider
def test_facebook_provider_auth_url_success():
provider = FacebookProvider({
'client_id': 'moose',
'client_secret': 'moose',
'redirect_uri': 'https://moose.com/callb... | ryannjohnson/popular-python | popular/providers/tests.py | Python | mit | 882 | [
"MOOSE"
] | f70ec82e3dea3ed85eba03e16f2b3524d6a198a08ff7d73d0042370232134938 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""Tests for the object filter functions."""
import unittest
from plaso.lib import errors
from plaso.lib import objectfilter
class DummyObject(object):
def __init__(self, key, value):
setattr(self, key, value)
class HashObject(object):
def __init__(self, hash_valu... | ostree/plaso | tests/lib/objectfilter.py | Python | apache-2.0 | 17,591 | [
"Desmond"
] | 4904526635dc9b27f2324a9e73aa97112f2b44bac8575021dbcd3b5d99d458f4 |
import random
import pandas as pd
import os
import sys
def rasl_probe_blast(read_file_path, blastn_path, db_path, print_on=False):
"""
This function returns blast results from queries optimized for rasl-seq conditions and outputs
a custom format
Parameters
----------
read_file_path: str, ... | SuLab/RASLseqAligner | src/RASLseqAlign.py | Python | mit | 4,792 | [
"BLAST"
] | 6a97fd59de0a748091405d3c5e195c391fd19dfb76f147e82225612ffc394397 |
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
def link_incompatible_error():
print("Reading in original prostate data.")
prostate = h2o.import_file(path=pyunit_utils.locate("smalldata/prostate/prostate.csv.zip"))
print("Throw error when trying to create... | pchmieli/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_DEPRECATED_link_incompatible_errorGLM.py | Python | apache-2.0 | 1,064 | [
"Gaussian"
] | a0162d1cff544962ba2ac0715ae0fa5a958f8436a8f35e82f4b754d332bf21b0 |
print("""
FEM simulation using getfem++ and siconos.
""")
import siconos.kernel as kernel
import getfemtosiconos as gts
import numpy as np
import getfem as gf
from matplotlib.pyplot import *
t0 = 0.0 # start time
T = 0.1 # end time
h = 0.005 # time step
g = 9.81 # gravity
e = 0.9 # restitution co... | bremond/siconos | examples/Mechanics/FEM/python/block.py | Python | apache-2.0 | 3,544 | [
"VTK"
] | dd078ce4d55dd4378cdfc65e068ab884e2f7958ca767074f34062d39b4e8c340 |
r"""OS routines for Mac, NT, or Posix depending on what system we're on.
This exports:
- all functions from posix, nt, os2, mac, or ce, e.g. unlink, stat, etc.
- os.path is one of the modules posixpath, ntpath, or macpath
- os.name is 'posix', 'nt', 'os2', 'mac', 'ce' or 'riscos'
- os.curdir is a string repres... | TathagataChakraborti/resource-conflicts | PLANROB-2015/seq-sat-lama/py2.5/lib/python2.5/os.py | Python | mit | 24,624 | [
"VisIt"
] | 73917980db3cabfcc96c7eb17b5f2e545afaf365ec270baac61b04dee6124cbb |
places = {
'CHARLOTTE, NC': {'lat': 35.206689, 'lng': -80.8127935},
'ANCHORAGE, AK': {'lat': 61.137705999999994, 'lng': -149.8490235},
'WICHITA, KS': {'lat': 37.694473, 'lng': -97.33458300000001},
'SACRAMENTO, CA': {'lat': 38.590199999999996, 'lng': -121.437659},
'DURHAM, NC': {'lat': 35.98744650000... | lnhubbell/tweetTrack | streamScript/webAPI/places.py | Python | mit | 6,514 | [
"COLUMBUS"
] | 722fa0fb10f236fdb769ec6ff39c853d7681ff27a23930e3edcc0f148df751b2 |
# BEGIN_COPYRIGHT
# END_COPYRIGHT
# pylint: disable=W0105, C0103
"""
..
Running Galaxy workflows
=========================
Run a workflow on a biobank object
----------------------------------
In this example we will run a simple galaxy workflow on biobank data
and save the results back in biobank.
FIXME Det... | crs4/omero.biobank | test/galaxy/try_run_workflow.py | Python | gpl-2.0 | 6,133 | [
"Galaxy"
] | 4eb949780f5bf396cfa67ebe447da3e6014a4f87d3bfbb23a8f89414b447775e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module defines the FeffInputSet abstract base class and a concrete
implementation for the Materials Project. The basic concept behind an input
set is... | aykol/pymatgen | pymatgen/io/feff/sets.py | Python | mit | 16,289 | [
"FEFF",
"pymatgen"
] | a12fd297419240de3c1f95d2458f6ea6407f3f81a5cc281e1c022d014913ce99 |
#!/usr/bin/python
import re
from numpy import array
import argparse
import sys
import csv
import pysam
import warnings
from operator import itemgetter, attrgetter
import itertools
from math import floor
#### This program is Copyright (C) 2013, Peter Hickey (peter.hickey@gmail.com) ####
## This program is free softwar... | PeteHaitch/bismark_v0.8.1 | comethylation_v3.py | Python | gpl-3.0 | 64,294 | [
"pysam"
] | 6178ea0eb6b7178d2a3086b4bad85a09d6a7111d18b8c72e1fcba78e28532732 |
#!/usr/bin/env python3
# Copyright (C) 2012-2017(H)
# Max Planck Institute for Polymer Research
#
# 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, eit... | espressopp/espressopp | examples/polystyrene_gromacs/polystyrene.py | Python | gpl-3.0 | 10,123 | [
"ESPResSo",
"Gromacs"
] | e7a9014c3fcdb0573d5ac19f19c4f18196696e194ae90049f88a7a5abc59534a |
"""
WSGI config for deployment project.
This module contains the WSGI application used by Django's development server
and any production WSGI deployments. It should expose a module-level variable
named ``application``. Django's ``runserver`` and ``runfcgi`` commands discover
this application via the ``WSGI_APPLICATION... | strets123/chembiohub_ws | deployment/wsgi.py | Python | mit | 1,388 | [
"RDKit"
] | 9c7338609bac74c2bda9cab34e251ada492306956bd6f87cf06635b595b8dade |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | liesbethvanherpe/NeuroM | neurom/view/tests/test_view.py | Python | bsd-3-clause | 7,449 | [
"NEURON"
] | fb4a9eac90f06e9e4bd842bb067e13286a0aa340a557d5c7333b292dd98c3fab |
# 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 RKeggrest(RPackage):
"""Client-side REST access to KEGG.
A package that provides a... | iulian787/spack | var/spack/repos/builtin/packages/r-keggrest/package.py | Python | lgpl-2.1 | 1,135 | [
"Bioconductor"
] | af8ac9814390ca642fae5497699c0170584a14e5981ed8be34ac154958d36725 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import re
from pymatgen import Structure, Lattice, Specie, DummySpecie
import numpy as np
"""
Classes for reading/writing mcsqs files following the rndstr.in format.
"""
__author__ = "Matthew Horton"
__copyri... | Bismarrck/pymatgen | pymatgen/io/atat.py | Python | mit | 4,422 | [
"CRYSTAL",
"pymatgen"
] | c148f9d73e6d237be7979465b3f44a85db3b2f7d3ad56dca7d6109dec7f0dcca |
#!/usr/bin/env python
"""
.. py:currentmodule:: FileFormat.Results.DetectorParameters
.. moduleauthor:: Hendrix Demers <hendrix.demers@mail.mcgill.ca>
MCXRay detector parameters from results file.
"""
# Script information for the file.
__author__ = "Hendrix Demers (hendrix.demers@mail.mcgill.ca)"
__version_... | drix00/pymcxray | pymcxray/FileFormat/Results/DetectorParameters.py | Python | apache-2.0 | 10,210 | [
"CRYSTAL"
] | 99f36701d0c201cfc73d917cd506d917b3496f04e367b9bc2ceb4efb79dcf743 |
#encoding:utf-8
"""The main classes used in Spacegrids are Field, Gr and Coord. They represent data defined on grids and reflect Netcdf data. Similar classes are Ax and AxGr.
Gr (grid) objects are constructed from Coord (coordinate) objects as tuples, and inherit methods related to the tuple members from the Membered... | willo12/spacegrids | spacegrids/fieldcls.py | Python | bsd-3-clause | 173,956 | [
"Gaussian",
"NetCDF"
] | 5708b85bb31ca37ed31244b86fcaf3f5e812dc25052384dadb4d156b42d68cae |
from views import *
from lookups import *
import requests
import re
from utils import *
import itertools
from config import config
if config.IMPORT_PYSAM_PRIMER3:
import pysam
import csv
#hpo lookup
import orm
from pprint import pprint
import os
import json
import pymongo
import sys
import re
import itertools
from ... | pontikos/phenopolis | views/individual.py | Python | mit | 23,176 | [
"pysam"
] | 0964128578c462a66b30ba50b8f76774b74c80966fc21652551e588a6fd057f4 |
#!/usr/bin/python
# coding=utf-8
"""
A script to extract subsequences starting from sequences in FASTA format.
Usage:
extract_subsequence.py --fasta_file test_files/test_sequences.fasta --output_file subsequences.fasta 10 20
This command will extract the nucleotides ranging in position 10 to 20 from all the ... | dvianello/mtdna-utils | extract_subsequence.py | Python | gpl-3.0 | 4,387 | [
"Biopython"
] | 0987065c596ae473ce21c2d95af282ab3e37417f1c4d3b8538f419667b4c3c46 |
import time, sys, os
import numpy as np
from scipy.linalg import LinAlgError
__all__ = ["lnlike_spec", "lnlike_phot", "chi_spec", "chi_phot", "write_log"]
def lnlike_spec(spec_mu, obs=None, spec_noise=None, f_outlier_spec=0.0, **vectors):
"""Calculate the likelihood of the spectroscopic data given the
spectr... | bd-j/prospector | prospect/likelihood/likelihood.py | Python | mit | 7,851 | [
"Gaussian"
] | 9d4668d204fd3f8f8a20d4de548b4ad9fd929c9b2cc0b86c67d8bd182a42451c |
#! /usr/bin/env python
import json
import sys
import os
# constants and default values
default_package = 'com.example';
default_visibility = 'private';
default_indent = ' '; # two spaces
beans_dir = 'beans/';
file_ext = '.java'
sep = ';\n';
package_prefix = 'package ';
package_suffix = ';\n\n';
import_string_line =... | vpmalley/gson-bean-gen | gson-bean-gen.py | Python | mit | 5,298 | [
"VisIt"
] | 5e858d74a98950996170747bb9b6eebd218eac7ea8d9d1af689c1e1096e7ea27 |
import sys
import os
import math
import re
from PyQt4 import QtGui, QtCore, Qt
#import pygraphviz as pgv
import networkx as nx
#sys.path.insert(0, '/home/harsha/BuildQ/gui')
import numpy as np
import config
import pickle
from default import *
from moose import *
sys.path.append('plugins')
from mplugin import *
from kk... | dilawar/moose-full | moose-gui/plugins/buildkkit.py | Python | gpl-2.0 | 27,013 | [
"MOOSE"
] | 6c82925ce22dfdd3057a62fa0c5d23ed313c2955336e4b25bb937182a3abfa5f |
# -*- coding: utf-8 -*-
"""Copyright 2015 Roger R Labbe Jr.
FilterPy library.
http://github.com/rlabbe/filterpy
Documentation at:
https://filterpy.readthedocs.org
Supporting book at:
https://github.com/rlabbe/Kalman-and-Bayesian-Filters-in-Python
This is licensed under an MIT license. See the readme.MD file
for mo... | barney-NG/pyCAMTracker | src/filterpy/stats/stats.py | Python | mit | 21,268 | [
"Gaussian"
] | 6eef5f58cc99947d80b661faf55aed44ad61757d75d9517525cd2f65b458678b |
# -*- coding: utf-8 -*-
"""
trueskill.mathematics
~~~~~~~~~~~~~~~~~~~~~
This module contains basic mathematics functions and objects for TrueSkill
algorithm. If you have not scipy, this module provides the fallback.
:copyright: (c) 2012-2015 by Heungsub Lee.
:license: BSD, see LICENSE for more deta... | Ninjakow/TrueSkill | lib/trueskill/mathematics.py | Python | gpl-3.0 | 8,593 | [
"Gaussian"
] | 8365fa0fa04c32bf1dfd73c12d95a190bf257cd15187eaeddf9dbd308c1455b3 |
# polling_location/controllers.py
# Brought to you by We Vote. Be good.
# -*- coding: UTF-8 -*-
from .models import PollingLocationListManager, PollingLocationManager
from config.base import get_environment_variable
from django.contrib import messages
import glob
import json
import requests
import wevote_functions.adm... | wevote/WebAppPublic | polling_location/controllers.py | Python | bsd-3-clause | 12,216 | [
"VisIt"
] | 7ce15254e9b9d4f55e504758b9ff5ac8cbe68c3f505f3129a816b3b39d569d1a |
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