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import pynacolada as pcd
from Scientific.IO import NetCDF
import os
import numpy as np
import pylab as pl
fnins = ['/home/hendrik/data/belgium_aq/rcm/aq09/stage1/int2lm/laf2009010100_urb_ahf.nc' , '/home/hendrik/data/belgium_aq/rcm/aq09/stage1/int2lm/laf2009010100_urb_ahf2.nc']
#print fnin
# fobjin = open(fnin,'rb')
#... | hendrikwout/pynacolada | old/examples/pynatestlist.py | Python | gpl-3.0 | 1,089 | [
"NetCDF"
] | a9f0ecc06069d57274391675191690e5e1707afa90b943a88c47ff94c1109d9f |
global XRFALLOWED
try:
from xrf_analysis import *
XRFALLOWED=True
except:
XRFALLOWED=False
import numpy, pylab, matplotlib
from xrd_math_fcns import *
from xrd_diffraction_conversion_fcns import *
from XRDdefaults import *
from xrf_depprof import *
import os
import time
import h5py
import operator
#import... | johnmgregoire/vanDover_CHESS | xrd_fileIO_fcns.py | Python | bsd-3-clause | 132,535 | [
"Gaussian"
] | b78e777d3a86e1590293f5caae91786967e7d23f7e92066ecf463e43c6098089 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2009-2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 Softw... | andrebellafronte/stoq | stoq/gui/update.py | Python | gpl-2.0 | 6,253 | [
"VisIt"
] | 0e35797558535ad3962d14759fd256f24cdefb871e08ac61f14ff43b3ebe5dfe |
# pyeq2 is a collection of equations expressed as Python classes
#
# Copyright (C) 2012 James R. Phillips
# 2548 Vera Cruz Drive
# Birmingham, AL 35235 USA
#
# email: zunzun@zunzun.com
# web: http://zunzun.com
#
# License: BSD-style (see LICENSE.txt in main source directory)
# Version info: $Id:... | JMoravec/unkRadnet | fitToCurve/pyeq2/Models_3D/Miscellaneous.py | Python | bsd-3-clause | 128,597 | [
"Gaussian"
] | 74f1139ad45dfe033f9152023a9917cde66e36208aa4e9ee5d0f5da62d8617bb |
# -*- coding: utf-8 -*-
"""
***************************************************************************
dataobject.py
---------------------
Date : August 2012
Copyright : (C) 2012 by Victor Olaya
Email : volayaf at gmail dot com
****************************... | m-kuhn/QGIS | python/plugins/processing/tools/dataobjects.py | Python | gpl-2.0 | 8,407 | [
"NetCDF"
] | 633f23a2666b4b2105b1c78a3b9cb96dfc82402c8508f09cb4abc5b321d27e59 |
import glob
import pandas as pd
import numpy as np
pd.set_option('display.max_columns', 50) # print all rows
import os
os.chdir("/gpfs/commons/home/biederstedte-934/evan_projects/correct_phylo_files")
normalB = glob.glob("binary_position_RRBS_normal_B_cell*")
mcell = glob.glob("binary_position_RRBS_NormalBCD19pCD27... | evanbiederstedt/RRBSfun | trees/chrom_scripts/total_chr03.py | Python | mit | 32,997 | [
"MCell"
] | 72e741284cfddb8e43c865af2519da4e1524ce026553043576113e9fb3c494cc |
from game_api import *
class ToyTree :
def __init__(self, label=None, score=None) :
self.score = score
self.label = label
self.children = []
self.zipper = []
self.sibling_index = None
# sibling index records how many left siblings this node has.
self.sibling... | jasonleaster/MIT_6.034_2015 | lab3/toytree.py | Python | gpl-2.0 | 6,112 | [
"VisIt"
] | 3deb7b8ad4a7b367027f69faa8eafcbca009fd3189d7c862fd97e4a3b408465a |
"""
This module holds the Layer class and its various subclasses:
Layer: Base class for layers. Defines interface and shared methods
PerceptronLayer: Layer subclass with a perceptron activation function
BoltzmannMachineLayer: Layer subclass with a Boltzmann Machine activation function
"""
from brio.misc.utils import o... | rueberger/brio | brio/blocks/layer.py | Python | gpl-2.0 | 20,103 | [
"Gaussian",
"NEURON"
] | a7f093bca5364d8a32525a21c5ce0e6189da469887aa58ed4fd6811102450370 |
<<<<<<< HEAD
from pymatgen.core.structure import Structure
=======
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
__author__ = "Matteo Giantomassi"
__copyright__ = "Copyright 2013, The Mate... | Bismarrck/pymatgen | pymatgen/io/xcrysden.py | Python | mit | 4,160 | [
"CRYSTAL",
"pymatgen"
] | c34b2f2e57620e98832b19f2c4df68b6ae57ecdee0f0c56ddebc8edb58b07311 |
#!/usr/bin/env python
# Install.py tool to download, unpack, build, and link to the LATTE library
# used to automate the steps described in the README file in this dir
from __future__ import print_function
import sys,os,re,subprocess,hashlib
# help message
help = """
Syntax from src dir: make lib-latte args="-b"
... | quang-ha/lammps | lib/latte/Install.py | Python | gpl-2.0 | 5,988 | [
"LAMMPS"
] | 4ba57a315a079e01eb96fa62b284c9ed4a4a531ff3b6c3b09933dfda7aa10802 |
from selenium.common.exceptions import NoSuchElementException
from datetime import datetime
from urllib import urlencode
# ============================================================================
class PrefixHandler(object):
def __init__(self, prefix, desc='Url Prefix Archiving Handler'):
self.prefix ... | ikreymer/browsertrix | web/handlers.py | Python | mit | 4,566 | [
"VisIt"
] | 4f2312711318bd56b1a136465f07b4dbb6a5442f7f662eaeeba43704d909cf17 |
import numpy as np
import visit_writer
if __name__ == '__main__':
print('# Start')
output = 'run.py3'
np.random.seed(0)
grid = np.array([-10., 10., 10, -10., 10., 10., 0., 0., 1.])
grid = np.reshape(grid, (3,3)).T
grid_length = grid[1] - grid[0]
grid_points = np.array(grid[2], dtype=np.int32)
num_p... | stochasticHydroTools/RotationalDiffusion | visit/test_visit.py | Python | gpl-3.0 | 2,516 | [
"VTK"
] | 8cc788da19323f6e9cea7d0c93c1bcbb1ca4d738c1a6b34dc0b053e498055414 |
"""
This is only meant to add docs to objects defined in C-extension modules.
The purpose is to allow easier editing of the docstrings without
requiring a re-compile.
NOTE: Many of the methods of ndarray have corresponding functions.
If you update these docstrings, please keep also the ones in
core/fromnum... | larsmans/numpy | numpy/add_newdocs.py | Python | bsd-3-clause | 217,825 | [
"Brian"
] | 6f337abc09582f3ec5b88d222004e8dcea6d4407a754419737ea9fa9d419f098 |
"""
VTK shortcut functions
For more about VTK, visit:
http://www.vtk.org/
http://www.vtk.org/Wiki/VTK/Examples/Python
"""
import vtk
import sys
import numpy
from vtk.util.colors import peacock
def vtk_point_cloud(points, colors=[], point_size=2):
"""
Represent a point cloud in VTK
Parameter... | sk1712/IRTK | wrapping/cython/irtk/ext/vtkTools.py | Python | bsd-3-clause | 17,980 | [
"VTK",
"VisIt"
] | fee1641d6152e85d5255cf96804bd7292186f941d1828132cc3c776d4b9a7ffb |
from scalars import *
def trig_test():
print(cos(Decimal('0.5')))
print(sin(Decimal('0.5')))
import math
print(math.cos(0.5))
print(math.sin(0.5))
def cos_test():
graph(lambda x: cos(pi*2*x))
#cos_test()
def v2f_test():
print(graph(v2f([1,1,1,1,1])))#should be dirac delta at 0
def integrate_... | AugurProject/augur-python | scalars_tests.py | Python | gpl-3.0 | 1,234 | [
"DIRAC"
] | aef849126dec254fa96e2679d03aea01f1cdccc7d5d96d603751476de5dd2478 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Unit tests and parser data tests for cclib."""
from data import *
| Schamnad/cclib | test/__init__.py | Python | bsd-3-clause | 268 | [
"cclib"
] | 49b1c25f0fcc325ff5aa02bfba8583c043e41b9e93108aaeb34afc041888dce5 |
"""Twisted shell support.
XXX - This module is missing proper docs.
"""
# Tell nose to skip this module
__test__ = {}
import sys
from twisted.internet import reactor, threads
from IPython.ipmaker import make_IPython
from IPython.iplib import InteractiveShell
from IPython.ipstruct import Struct
import Queue,thread,... | mastizada/kuma | vendor/packages/ipython/IPython/twshell.py | Python | mpl-2.0 | 9,871 | [
"Brian"
] | 9242568195316f67aa5e27c18a33b5a1f8314825a52ec9955134610d33c8605d |
# choco/_ast_util.py
# Copyright (C) 2006-2016 the Choco authors and contributors <see AUTHORS file>
#
# This module is part of Choco and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""
ast
~~~
The `ast` module helps Python applications to process trees of the P... | whiteclover/Choco | choco/_ast_util.py | Python | mit | 25,694 | [
"VisIt"
] | c5a707a2d32a9df3a1bd56ec1f5c047ef7ccd2f47517896f5b47d6e01a1992d6 |
# 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 PyPhonopy(PythonPackage):
"""Phonopy is an open source package for phonon
calculations... | iulian787/spack | var/spack/repos/builtin/packages/py-phonopy/package.py | Python | lgpl-2.1 | 835 | [
"phonopy"
] | 3c8449d57bff308e77005c3bd23fa13e815d2a201e8b76ea612783522fc9942f |
from __future__ import print_function
import sys
import numpy as np
msg = "\n'TypeError: array cannot be safely cast to required type'\n"
msg += "means you are probably using a broken ScientficPython, \n"
msg += "see: https://bugs.launchpad.net/ubuntu/+source/python-scientific/+bug/1041302\n"
import Scientific.IO.Ne... | suttond/MODOI | ase/test/scientificpython_bug.py | Python | lgpl-3.0 | 814 | [
"NetCDF"
] | ebaf60ee75a175ce27277499797ebf0bedac779583e183b6b71250634bcef647 |
"""
This Code replaces usage of another pipeline that was also detected SNPs between the referrnce COI to sequncing data.
For backward-compatibility it outputs few NA columns
"""
from Bio.SeqIO import parse
from optparse import OptionParser
def Main():
parser = OptionParser()
parser.add_option("--db_file",
... | omerzu/larvae_project | scripts/simple_coverage_calculator.py | Python | mit | 3,160 | [
"BLAST"
] | 9a67361053a9f2ab80d4782fa39b83ecf2e4862766268339f42127829f7c3dda |
# gp_signals.py
"""Contains class factories for Gaussian Process (GP) signals.
GP signals are defined as the class of signals that have a basis
function matrix and basis prior vector..
"""
import functools
import itertools
import logging
import numpy as np
import scipy.sparse as sps
from sksparse.cholmod import chole... | nanograv/enterprise | enterprise/signals/gp_signals.py | Python | mit | 31,619 | [
"Gaussian"
] | e59b37a99ebdba9b5f5fae3f9d762a5da97cba3732b534c77c22252802b97da8 |
from lettuce import *
from rapidsms.contrib.locations.models import *
from survey.features.page_objects.batches import AddBatchPage
from survey.features.page_objects.batches import AssignQuestionToBatchPage
from survey.features.page_objects.batches import BatchListPage
from survey.features.page_objects.batches import ... | unicefuganda/uSurvey | survey/features/Batch-steps.py | Python | bsd-3-clause | 14,663 | [
"VisIt"
] | 20ade3d047b8fddda69e00d06984e4953ee4b736e871c58ebb19a393a819a31e |
# coding: utf-8
#!/usr/bin/env python
from __future__ import division, unicode_literals
"""
#TODO: Write module doc.
"""
__author__ = 'Shyue Ping Ong'
__copyright__ = 'Copyright 2013, The Materials Virtual Lab'
__version__ = '0.1'
__maintainer__ = 'Shyue Ping Ong'
__email__ = 'ongsp@ucsd.edu'
__date__ = '8/1/15'
i... | rousseab/pymatgen | pymatgen/io/feffio.py | Python | mit | 484 | [
"FEFF",
"pymatgen"
] | ce1fb5ba93da7d42f332d8ef1e482b6aa20fcb7b8dcdfc056db88de1033c13bc |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
from collections import OrderedDict
import itertools
import warnings
import re
from ast import literal_eval
import nump... | Bismarrck/pymatgen | pymatgen/io/lammps/data.py | Python | mit | 35,466 | [
"LAMMPS",
"pymatgen"
] | 468c5cef801528034ca65e10b674d926f5dd08e740225665a8fc0a412ff60623 |
from nbodykit.base.mesh import MeshFilter
import numpy
class TopHat(MeshFilter):
""" A TopHat filter defined in Fourier space.
Notes
-----
A fourier space filter is different from a configuration space
filter. The TopHat in fourier space creates ringing effects
due to the ... | nickhand/nbodykit | nbodykit/filters.py | Python | gpl-3.0 | 1,301 | [
"Gaussian"
] | 9456001c4cddc52f61c86f4bb6a231d690197193e3e9cca0203a6a3de2513e52 |
# (c) 2015 - Jaguar Land Rover.
#
# Mozilla Public License 2.0
#
# Python-based life cycle manager PoC
import gtk
import dbus
import dbus.service
from dbus.mainloop.glib import DBusGMainLoop
import sys
import time
import swm
import settings
import logging
import os
import getopt
import daemon
logger = logging.getLo... | rstreif/genivi_software_management | lifecycle_manager/lifecycle_manager.py | Python | mpl-2.0 | 4,711 | [
"Jaguar"
] | d3662f5166712d01a35aff5af59d79b11d102009ea1ad184551450aa154f69f4 |
########################################################################
# File: RequestDB.py
# pylint: disable=no-member
########################################################################
""" Frontend for ReqDB
:mod: RequestDB
=======================
.. module: RequestDB
:synopsis: db holdin... | DIRACGrid/DIRAC | src/DIRAC/RequestManagementSystem/DB/RequestDB.py | Python | gpl-3.0 | 34,747 | [
"DIRAC"
] | 1593b298b86043f021eade8456c9d27b51d3baacccc840d2dda94ee0ec032fd9 |
# -*- coding: utf-8 -*-
#
# pymatgen documentation build configuration file, created by
# sphinx-quickstart on Tue Nov 15 00:13:52 2011.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# Al... | migueldiascosta/pymatgen | docs/conf.py | Python | mit | 9,424 | [
"pymatgen"
] | edbb2e20dfd1f6fa94c98a97a0dae9d088ffd7b5446ce396858d0f55f30413e8 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# submitjob - job submit page
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publi... | heromod/migrid | mig/cgi-bin/submitjob.py | Python | gpl-2.0 | 1,098 | [
"Brian"
] | 9cd2ebb01ef3e49bcc093d756438c6821e83b7edd34b1425abc50b2d0a0fccef |
'''
Contains physical constants used in snow modeling.
@var a_gravity: Gravitational acceleration [m s-2]
@var eta0: Viscosity of snow at T=0C and density=0 [N s m- 2 = kg m-1 s-1]
@var rho_air: Density of air [kg m-3], dry air at 0 C and 100 kPa
@var rho_water: Density of water [kg m-3]
@var rho_ice: Density o... | kmunve/pysenorge | pysenorge/constants.py | Python | gpl-3.0 | 1,844 | [
"Avogadro"
] | 7fd2a550fa5f09255626bc147e12f325e49f6c2d0982079967b01f8a458c3597 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/main.py | Python | gpl-3.0 | 1,299 | [
"ORCA"
] | 3e9a66e32dbbccabcbbf1e6bfaeafbdb2759a3bdb75fb6af31095afbeb189b7f |
import matplotlib.pyplot as plt
from numpy import linspace
import sys
user_filename = raw_input("Please state filename of results: ")
f = open(user_filename,"r")
lines = f.readlines()
u = []
f_exact = []
v = []
epsilon = []
u2 = []
for line in lines:
u.append(line.split(' ')[1])
f_exact.append(line.split(' ')[2... | linegpe/FYS3150 | Project1/plot_results.py | Python | gpl-3.0 | 750 | [
"Gaussian"
] | d89dab0b4b5dbef12fd2fafe6c20a7eadfac9908d1a9e9120d0ee38ae11181fa |
import sys
import numpy as np
import pandas as pd
from joblib import Parallel, delayed
from sklearn.preprocessing import MinMaxScaler
from pystruct.models import StructuredModel
from pystruct.learners import OneSlackSSVM
sys.path.append('.')
from shared import LOG_SMALL, LOG_TRANSITION, FEATURES # noqa: E402
class ... | cdawei/digbeta | dchen/tour/src/ssvm_nf.py | Python | gpl-3.0 | 19,817 | [
"VisIt"
] | a8f6327b96bbdf740664577a1cb231ac82c9a00b179bf6d7d7456b194c039325 |
"""Base Tornado handlers for the notebook.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, distributed as p... | marcoantoniooliveira/labweb | oscar/lib/python2.7/site-packages/IPython/html/base/handlers.py | Python | bsd-3-clause | 14,220 | [
"Brian"
] | 8df8dda09efe3c8ee4411dbf83a9ebe868e76b507743cca6eb362e46c136ae75 |
# Python3 code
# Made by: Yan Zhiqiang & Tereza Jerabkova
# An example file that construct galaxy-wide IMF according to the input parameters in file "input_parameters.txt"
# The outputs of this example are:
# - the comparison plot of galaxy-wide IMF, canonical IMF, and the histogram of stellar masses (optional);
# ... | Azeret/galIMF | igimf_calculator.py | Python | gpl-3.0 | 12,511 | [
"Galaxy"
] | d02b3b528b550b73283f64d32d4df1aa218f3c51cca438d9a8463c3b7474cd22 |
#! /usr/bin/env python
import sys
from optparse import OptionParser
from datetime import datetime
from itaps import iMesh, iBase
def get_centers_and_vals(filename, outfile, valtagname, errtagname, plotnum, \
header):
"""
"""
imesh = iMesh.Mesh()
imesh.load(filename)
cnt = 0
ta... | svalinn/meshtools | tetmesh2points/tet_vals_and_centroids.py | Python | bsd-2-clause | 4,156 | [
"VTK"
] | 5be3df534926eeacb7e96f7154016c05d6e3eea1de28afa560eabc4687f4f5e9 |
import cellprofiler.icons
from cellprofiler.gui.help import PROTIP_RECOMEND_ICON, PROTIP_AVOID_ICON, TECH_NOTE_ICON
__doc__ = '''<b>Export To Database</b> exports data directly to a database, or in
database readable format, including an imported file
with column names and a CellProfiler Analyst properties file, if de... | LeeKamentsky/CellProfiler | cellprofiler/modules/exporttodatabase.py | Python | gpl-2.0 | 210,109 | [
"CDK"
] | 02a67c0a2af6eb146f14c492471d03c2eb59b61968bda987813c04798ae5d86c |
import hashlib
import os
import posixpath
import stat
import re
from fnmatch import filter as fnfilter
from six import string_types
from fabric.state import output, connections, env
from fabric.utils import warn
from fabric.context_managers import settings
# TODO: use self.sftp.listdir_iter on Paramiko 1.15+
def... | xLegoz/fabric | fabric/sftp.py | Python | bsd-2-clause | 13,012 | [
"VisIt"
] | 56c54554ea5befed29e670e7175a54e429841a40da8fef878e8219d13b29d1ac |
#!/usr/bin/env python3
### VERY MUCH PYTHON 3 !!!
"""
Example for aiohttp.web basic server
Uses a background timer to read from a file to update a shared datastructure
Because it's going to be used as a simulator
Made available under the MIT license as follows:
Copyright 2017 Brian Bulkowski brian@bulkowski.org
P... | bbulkow/MagnusFlora | rest/jarvis.py | Python | mit | 13,536 | [
"Brian"
] | 5a21a78f0dc8ac0c24947efb9b3cc1dc24f724190843af9bb04b13952b956c3e |
# Copyright 2012 Nebula, Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agree... | tqtran7/horizon | horizon/base.py | Python | apache-2.0 | 38,181 | [
"VisIt"
] | 89d1bc02b32b8cf458ae62e02f80263d534c2f3196e396cd650fbb09b42f9a6a |
#!/usr/bin/env python
import os
from StringIO import StringIO
import sys
import unittest
import pyrapi
import tseal.test_utils as test_utils
from seal.lib.aligner.hirapi import HiRapiAligner, HiRapiOpts
class TestHiRapiProperties(unittest.TestCase):
def setUp(self):
self.hi = HiRapiAligner('rapi_bwa')
... | crs4/seal | tests/tseal/lib/aligner/test_hirapi.py | Python | gpl-3.0 | 6,120 | [
"BWA"
] | d6903bf40e776ea82c53a5e2b0ba3e40e046cbaeb7b861176f4da9ffc4d78c2a |
# -*- coding: utf-8 -*-
# Copyright 2022 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... | googleapis/python-private-catalog | tests/unit/gapic/privatecatalog_v1beta1/test_private_catalog.py | Python | apache-2.0 | 81,898 | [
"Octopus"
] | f629e3ab02ccad9d78af50b5968974166a7aee49d860bbaa696c2c7b5ef06f73 |
import pandas as pd
import mdtraj as md
from ace_x_y_nh2_parameters import *
larger = pd.read_csv("./data/larger_couplings.csv")
smaller = pd.read_csv("./data/smaller_couplings.csv")
reference = []
for aa in amino_acids:
value = smaller.ix["G"][aa]
xyz = ["G%s" % aa, 0, value]
reference.append(xyz)
... | choderalab/open-forcefield-group | nmr/ace_x_y_nh2/code/analyze_scalar_couplings.py | Python | gpl-2.0 | 1,531 | [
"MDTraj"
] | 009772de2e27d7afdd97ca976992020201c204fd1aa35015567593e434d068f6 |
""" ResourceStatus
Module that acts as a helper for knowing the status of a resource.
It takes care of switching between the CS and the RSS.
The status is kept in the RSSCache object, which is a small wrapper on top of DictCache
"""
from __future__ import absolute_import
from __future__ import division
from __future_... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/Client/ResourceStatus.py | Python | gpl-3.0 | 14,021 | [
"DIRAC"
] | 2984bd3fbbd756e4ba012c2280a57e7c5b4a8812a3aceb37a460ace79401dacf |
from PyQt5 import QtCore
from PyQt5 import QtGui
from PyQt5 import QtWidgets
from PyQt5.Qt import Qt
class WorldView(QtWidgets.QWidget):
def __init__(self, scale, parent):
super(WorldView, self).__init__(parent)
self.world = parent.world
self.resize(self.world.area[0], self.world.area[1])
... | jroivas/moose-mating | qworld.py | Python | gpl-3.0 | 2,435 | [
"MOOSE"
] | 6be9dec84d6a807336c5507913b33ebb487afba1325ff7ffedaf6a881daa827d |
import sys
py_ver = sys.version_info[0] + ( sys.version_info[1] / 10.0 )
if py_ver < 3.5:
raise "Must be using Python 3.5 or better"
import os
import time
# this helps me know how long in time a file will play
import wave
import random
import platform
import subprocess
"""
A player of our sounds
Sound files ... | bbulkow/MagnusFlora | samples/sound.cmd.py | Python | mit | 4,356 | [
"Brian"
] | 37d5261a67d9eb4b077811d190a2ae29ab5c07ea903afc0fc3ff6611d48fbac5 |
"""Ansible specific pylint plugin for checking format string usage."""
# (c) 2018, Matt Martz <matt@sivel.net>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
imp... | nitzmahone/ansible | test/lib/ansible_test/_util/controller/sanity/pylint/plugins/string_format.py | Python | gpl-3.0 | 3,124 | [
"VisIt"
] | ff85b46047961e6ad1c1f825412b43f61d7602aacbe79914787d9871dbc61622 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2007 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/lib/diffutils.py | Python | gpl-2.0 | 2,742 | [
"VisIt"
] | 7e9b73f476b97bc043c045cb21bda864db83e24cfbe855338fec8e0f0082aaab |
# -*- coding: utf8 -*-
# Copyright (C) 2015 - Philipp Temminghoff <phil65@kodi.tv>
# This program is Free Software see LICENSE file for details
from __future__ import absolute_import
from __future__ import unicode_literals
from builtins import str
import urllib
import xbmcgui
from resources.lib import Utils
from... | phil65/script.maps.browser | resources/lib/GooglePlaces.py | Python | gpl-2.0 | 7,111 | [
"CASINO"
] | 6ced6431afd4c3bc5fc71294b428dd380a39a00faef5f492137508181d2a64f5 |
"""A setuptools based setup module.
See:
https://packaging.python.org/en/latest/distributing.html
https://github.com/pypa/sampleproject
"""
# Always prefer setuptools over distutils
import setuptools
# To use a consistent encoding
import codecs
import os
here = os.path.abspath(os.path.dirname(__file__))
# Get the lo... | dupgit/versions | setup.py | Python | gpl-3.0 | 7,035 | [
"VisIt"
] | dcc9a7e379ba439fc386c71b727896361628700daf949a1952d00043c2688c26 |
import pytest
import random
from pyshare import group, party, expense, payment
# Create test data.
group_names = ["Alfa", "Bravo", "Charlie", "Delta", "Echo", "Foxtrot", "Golf", "Hotel", "India", 'Juliett',
"Kilo", "Lima", "Mike", "November", "Oscar", "Papa", "Quebec", "Romeo", "Sierra", "Tango",
... | rosemichaele/pyshare | tests/test_group.py | Python | gpl-3.0 | 4,723 | [
"Brian"
] | 79470b6a685bb38355914795890856197519d198aea26ff54a39cdc3ed35e465 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
from sisl._internal import set_module
from ..sile import Sile, SileCDF, SileBin
__all__ = ['SileOpenMX', 'SileCDFOpenMX... | zerothi/sisl | sisl/io/openmx/sile.py | Python | mpl-2.0 | 547 | [
"OpenMX"
] | 8cf2972d445f53cc6bb1bf70315825f37f6f53e731e717d06c9b724e1826c198 |
#!/usr/bin/python
# (c) 2017, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
# most of it copied from AWX's scan_packages module
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': ... | Dhivyap/ansible | lib/ansible/modules/packaging/os/package_facts.py | Python | gpl-3.0 | 13,128 | [
"Brian"
] | b33c702511b9f588aace9a88a061321a111984a86abb5e958a71d5439a0dea0c |
# -*- coding: utf-8 -*-
"""
Created on Wed Dec 2 2015
Library for MG_Synth. Defines functions for reading motifs, generating
synthetic DNA sequences, computing likelihoods, etc
@author: ivanerill
"""
#The following code assumes that Biopython is installed
from Bio.Seq import Seq
from Bio import motifs
from Bio.Alph... | ErillLab/CogsNormalizedPosteriorProbabilityThetas | MGtest/MG_synth_lib.py | Python | gpl-3.0 | 16,106 | [
"Biopython"
] | 30fc33e3b8fc9968278856c0f6d7e39327455eff124ca328a67bfd0bfab09206 |
from ase import Atoms
from gpaw import GPAW
from gpaw.wavefunctions.pw import PW
from gpaw.test import equal
for mode in ['fd', 'pw']:
print mode
hydrogen = Atoms('H',
cell=(2.5, 3, 3.5),
pbc=1,
calculator=GPAW(txt=None, mode=mode))
hydrogen.ge... | ajylee/gpaw-rtxs | gpaw/test/potential.py | Python | gpl-3.0 | 1,104 | [
"ASE",
"GPAW"
] | e01bcb7bee845153601ed9795eb5d7088130650ccca1f0a8752b0b5e8a396326 |
# Copyright (c) 2012 Spotify AB
#
# 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, s... | drincruz/luigi | setup.py | Python | apache-2.0 | 2,826 | [
"VisIt"
] | 85d34f837a4782c88291432751f757339cbfbf6d4d9206f58cd09b925f39ec64 |
import COPASI
import sys
dm = COPASI.CRootContainer.addDatamodel()
def checkModel(file_name):
if not dm.loadModel(file_name):
dm.importSBML(file_name)
a = COPASI.CModelAnalyzer(dm.getModel())
res = a.getReactionResults()
for result in res:
if result.hasIssue(): # only output problematic reactions
... | jonasfoe/COPASI | copasi/bindings/python/examples/checkModel.py | Python | artistic-2.0 | 534 | [
"COPASI"
] | 37fe328cfb96bf1b2a1ceaacbeb07f0343f7ac537588d8fe050a65ce015ba28d |
# -*- coding: utf-8 -*-
from .NeuroML import NeuroML, loadNeuroML_L123
from .NetworkML import NetworkML
from .MorphML import MorphML
from .ChannelML import ChannelML
import tempfile
import logging
debug_ = False
if debug_:
logging.basicConfig(level=logging.DEBUG,
format='%(asctime)s %(name)-12s %(levelna... | dharmasam9/moose-core | python/moose/neuroml/__init__.py | Python | gpl-3.0 | 954 | [
"MOOSE"
] | 48c16453b957c5ca9a6e5bcb18954fbb8843356f9a90fb7616b7e355e48f3b9e |
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
def offset_gaussian():
# Connect to a pre-existing cluster
insurance = h2o.import_file(pyunit_utils.locate("smalldata/glm_test/insurance.csv"))
insurance["offset"] = insurance["Holders"].log()
from h2o.estimators.gbm impor... | pchmieli/h2o-3 | h2o-py/tests/testdir_algos/gbm/pyunit_offset_gaussian_gbm.py | Python | apache-2.0 | 1,982 | [
"Gaussian"
] | fce15197055c320955ae284ff3b780a105d53d949b0fd3d5bc96a3c7b889987b |
#!/usr/bin/python
'''
Script to find a route through an SSW sector map
'''
# Copyright 2009, 2015-2016 Squiffle
from __future__ import absolute_import
from __future__ import print_function
import ssw_sector_map2 as ssw_sector_map
import ssw_map_utils, ssw_societies, ssw_utils
import operator, sys, getopt, datetime
... | UEWBot/ssw-scripts | ssw_route.py | Python | gpl-3.0 | 6,954 | [
"VisIt"
] | e96305a567ee2bc91c3541ba715c19d9235cf25ce212ff8c84f830374e17dfdf |
from distutils.core import setup
DESCRIPTION = "General tools for Astronomical Time Series in Python"
LONG_DESCRIPTION = """
nufftpy: Non-Uniform FFT in Python
==================================
This is a pure python implementation of the NUFFT.
For more information, visit http://github.com/jakevdp/nufftpy
"""
NAME =... | jakevdp/nufftpy | setup.py | Python | bsd-2-clause | 1,442 | [
"VisIt"
] | 67fc01cdf85738e2decb7cc1c461af2243f33a25975a0e2d10546f8de3669af7 |
#!/usr/bin/env python
# This example demonstrates how to use 2D Delaunay triangulation.
# We create a fancy image of a 2D Delaunay triangulation. Points are
# randomly generated.
import vtk
from vtk.util.colors import *
# Generate some random points
math = vtk.vtkMath()
points = vtk.vtkPoints()
for i in range(0, 50)... | naucoin/VTKSlicerWidgets | Examples/Modelling/Python/DelMesh.py | Python | bsd-3-clause | 2,665 | [
"VTK"
] | 38a0da65f02ac5353f0cc074eddd02d6ce01987eb4e997205bcf3fff03b181be |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | espressomd/espresso | testsuite/scripts/samples/test_minimal-charged-particles.py | Python | gpl-3.0 | 1,024 | [
"ESPResSo"
] | 340779d1e053141e48281d9f1fbb0165d71d3acf31c88602b5706051626430a5 |
"""HTTPS module based on the GFAL2_StorageBase class."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# from DIRAC
from DIRAC.Resources.Storage.GFAL2_StorageBase import GFAL2_StorageBase
from DIRAC import gLogger
class GFAL2_HTTPSStorage(GFAL2_StorageBa... | yujikato/DIRAC | src/DIRAC/Resources/Storage/GFAL2_HTTPSStorage.py | Python | gpl-3.0 | 980 | [
"DIRAC"
] | d8979328223b14be9a3e6642460dd51193819591408d989ad52d5328bbafec6c |
#!/usr/bin/python
# Copyright: (c) 2017, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
'status': ['st... | orgito/ansible | lib/ansible/modules/files/xattr.py | Python | gpl-3.0 | 6,842 | [
"Brian"
] | f05307811f326a943066cc1c3a9c1e168fb58716d31d38a4619497270876e556 |
##############################################################################
# pymbar: A Python Library for MBAR
#
# Copyright 2016-2017 University of Colorado Boulder,
# Copyright 2010-2017 Memorial Sloan-Kettering Cancer Center
# Portions of this software are Copyright (c) 2010-2016 University of Virginia
#
# Autho... | choderalab/pymbar | pymbar/exp.py | Python | mit | 10,191 | [
"Gaussian"
] | 9c506d003422e77cb9d40c1c9da7536d08d7f07447559b06da92418c7739da6b |
import numpy as np
import matplotlib.pyplot as plt
from iterative_policy_evaluation import print_values, print_policy
from grid import standard_grid, negative_grid
from monte_carlo_random import play_game, random_action, EPS, GAMMA, ALL_POSSIBLE_ACTIONS
LEARNING_RATE = 0.001
if __name__ == '__main__':
grid = stan... | InnovArul/codesmart | Assignments/Jul-Nov-2017/reinforcement_learning_udemy/rl/monte_carlo_approximation.py | Python | gpl-2.0 | 1,822 | [
"VisIt"
] | 6f9d9200a4bb73e73d66a8892d2f86708cceacf887542d81267ee45199b2be8d |
import os.path as osp
work_dir = "/home/salotz/Dropbox/devel/mastic/work/pi_stacking"
ref_benzene_PDB_path = osp.join(work_dir, "ref_benzene.pdb")
ref_benzene_MOL_path = osp.join(work_dir, "benzene.mol")
from rdkit import Chem
ref_benzene_PDB_rdkit = Chem.MolFromPDBFile(ref_benzene_PDB_path, removeHs=False, sanitiz... | salotz/mast | work/pi_stacking/make_benzenebenzene_systemtype_pkl.py | Python | mit | 2,758 | [
"RDKit"
] | 53e94702c24e2b869404053e4316f7c8db1b978ffd6af92fd01ccafe633682d7 |
"""User API view functions"""
from datetime import datetime
from dateutil.relativedelta import relativedelta
from flask import (
Blueprint,
abort,
current_app,
jsonify,
make_response,
redirect,
request,
session,
url_for,
)
from flask_babel import force_locale
from flask_user import ... | uwcirg/true_nth_usa_portal | portal/views/user.py | Python | bsd-3-clause | 79,010 | [
"VisIt"
] | a6eac7adcccf2bfdf6f73d8e08ac9bfa483e773c30b9173e4efadba6dae5ab4a |
########################################################################
# This example demonstrates synaptic summation in a branched neuron.
# Copyright (C) Upinder S. Bhalla NCBS 2018
# Released under the terms of the GNU Public License V3.
########################################################################
impo... | BhallaLab/moose-examples | tutorials/Electrophys/ephys3_synaptic_summation.py | Python | gpl-2.0 | 17,152 | [
"MOOSE",
"NEURON"
] | 56d17e4035398e00f2a2d78285498c64fef822500d4a62995dbcda82f282f7ee |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/view/controls/editors/richtexteditor.py | Python | gpl-2.0 | 12,882 | [
"VisIt"
] | 3e276677cd46ac547b1606c91489a9f2454e27fc57db62dee941c749fee0762d |
"""Main entry point for distributed next-gen sequencing pipelines.
Handles running the full pipeline based on instructions
"""
from __future__ import print_function
from collections import defaultdict
import copy
import os
import sys
import resource
import tempfile
import toolz as tz
from bcbio import log, heterogen... | chapmanb/bcbio-nextgen | bcbio/pipeline/main.py | Python | mit | 27,572 | [
"Bowtie"
] | e0545f035a77d29895989c663deb2cc7e387549721f6c12da959858148c56b00 |
"""
Bok choy acceptance tests for problems in the LMS
"""
from textwrap import dedent
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.lms.courseware import CoursewarePage
from ... | edx/edx-platform | common/test/acceptance/tests/lms/test_lms_problems.py | Python | agpl-3.0 | 7,716 | [
"VisIt"
] | f1725f2a2f86cc13afe29db48aac8f62e6134beb18bb82d74de258b655819a21 |
# coding=utf-8
# Copyright 2018 The DisentanglementLib 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
#
# Un... | google-research/disentanglement_lib | disentanglement_lib/methods/unsupervised/vae.py | Python | apache-2.0 | 16,472 | [
"Gaussian"
] | 921ed5aaecb9b035521cba2b801aaeeb51d9b75162fe313adc49859eddffff25 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Perform fragmentation of molecules.
"""
import logging
import copy
from monty.json import MSONable
from pymatgen.analysis.graphs import MoleculeGraph, MolGraphSplitError
from pymatgen.analysis.local_env im... | mbkumar/pymatgen | pymatgen/analysis/fragmenter.py | Python | mit | 19,035 | [
"pymatgen"
] | ec9446be44af69e309afb3be7bc94ab76ad75f43a492035d1f45d66230b0ddc0 |
# coding=utf-8
import telegram
import telegram.ext
import config
import datetime
import utils
import urllib
import html
import logging
import time
import magic
import os
import re
import mimetypes
import pydub
import threading
import traceback
import base64
from . import db, speech
from .whitelisthandler import Whiteli... | RoyXiang/ehForwarderBot | plugins/eh_telegram_master/__init__.py | Python | gpl-3.0 | 63,061 | [
"VisIt"
] | 3c55b58da82807dd62bd5155b98e45db5b7da4ffa3995586d8675968bcc0a557 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | src/pylada/crystal/readCif.py | Python | gpl-3.0 | 55,318 | [
"CRYSTAL",
"VASP"
] | 887d43753a9a399658cb5ab598c5dcf4b69d8d2b68929b74dee3362005539c35 |
#!/usr/bin/env python
# VTK Viewer
# Written 2012-2013 Hal Canary <http://cs.unc.edu/~hal>
# Copyright 2012-2013 University of North Carolina at Chapel Hill.
#
# 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... | HalCanary/vtkviewer | vtkviewer.py | Python | apache-2.0 | 11,787 | [
"ParaView",
"VTK"
] | c73ad032d7af281494239de73fc0a2b297913e4adf04563e26287e68440e95e1 |
# Find regions that have zero coverage
# Copyright (C) 2015 Harold Pimentel
#
# 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 ver... | pachterlab/kma | inst/pre-process/zeroCoverage.py | Python | gpl-2.0 | 7,172 | [
"pysam"
] | 0e2a31f2154c33fee7370d2242bf2bab6105a3ce12710d5baf585c130f549e79 |
import socket
import sys
import base64
answers = {
'0264cf610d20d90ced78d4f1ca621763ea183234c20f12d00fe1171074e71ba3': 'nic Fronti',
'02a1deee284afc3acd59d1b68cf5c9ad40e4ccf47ba99db55e38df8f1136ef5e': 'g plans, dictating voicemail. P',
'02a72b19e546bc4ef56610c1f5c200ccef462907241a22909fbe341da20d92a2': 'assed it to me... | sinfocol/ctfs | writeups/2017/defcon-qualifiers/crackme-2000/sorcery.py | Python | gpl-3.0 | 20,475 | [
"VisIt",
"exciting"
] | 08f5825df7e14f3f8892de1bc86f4c31d806dc740626d44a56567f29279a5ba1 |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. 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
#
# U... | gkc1000/pyscf | pyscf/cc/test/test_2e.py | Python | apache-2.0 | 2,031 | [
"PySCF"
] | af22d8f74c6474e3bbab4cd8c02e89150cd2af68fa5461b9228b3405c5d062d7 |
# # #
# 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/tas_cld_cru_ts31_to_cl20_downscaling.py | Python | mit | 23,577 | [
"NetCDF"
] | 0707cb53dda80aec439d85642f4de50254d07b8fe8e3fd6e4a902b044f181893 |
#!/usr/bin/env python
import numpy as np
import tex2elas
import CijUtil
def read_texture_file(filename):
"""Read data from a theia texture file"""
# Deal with compressed files.
import os
if (os.path.splitext(filename)[1] == '.gz'):
import gzip
f = gzip.open(filename, 'rb')
el... | andreww/theia_tools | theiaptfile.py | Python | mit | 10,323 | [
"CRYSTAL"
] | a5c9c73a41082e0d7529aeb8f88abe416312552468a0065189a6fbd58ca9f233 |
'''
Import Guardian articles from JSON
'''
import sys
reload(sys)
sys.setdefaultencoding('utf-8')
import os
import json
import re
from urllib import unquote
from elasticsearch import helpers
sys.path.insert(0,'../')
from models.article import Article
from controllers.sentimentExtractor import SentimentExtractor
from... | ControCurator/controcurator | cronjobs/importSocMed.py | Python | mit | 13,308 | [
"VisIt"
] | 58254bc16cc4e37c6ec800e4c887224c35b255cfe3811c19a0cb87ae482794cf |
#!/bin/env python3
import sys
import os
if len(sys.argv) < 2:
print('')
print('Usage: %s POSCAR gjf_file1 gjf_file2 ...' % sys.argv[0].split('/')[-1])
print('')
exit(1)
print('############### Replacing images with gvfile ###############')
print('')
os.system('gjf2vas.py %s > /dev/null' % (' '.join(s... | Mabinogiysk/VASP-script | nebgjf2vas.py | Python | gpl-2.0 | 622 | [
"VASP"
] | 7e33c5e17fde5b0e2ff92f542a9d741d3e9c41b16ecd40942c7dc7aec09477e2 |
# -*- coding: utf-8 -*-
"""Algorithms for spectral clustering"""
# Author: Gael Varoquaux gael.varoquaux@normalesup.org
# Brian Cheung
# Wei LI <kuantkid@gmail.com>
# License: BSD 3 clause
import warnings
import numpy as np
from ..base import BaseEstimator, ClusterMixin
from ..utils import check_rand... | huzq/scikit-learn | sklearn/cluster/_spectral.py | Python | bsd-3-clause | 24,295 | [
"Brian",
"Gaussian"
] | 5a4ad881c717f3db34b2b4abb57930d67e3707447b4cadb2861a3627fbddfbda |
# This file is part of the Trezor project.
#
# Copyright (C) 2012-2018 SatoshiLabs and contributors
#
# This library is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License version 3
# as published by the Free Software Foundation.
#
# This library is distrib... | romanz/python-trezor | trezorlib/client.py | Python | lgpl-3.0 | 13,041 | [
"VisIt"
] | 3b307c6816b661ce2abf4ce39391fc8d88e6a3e3d11a46902cdddf0f5e92cf2b |
""" BHMM: A toolkit for Bayesian hidden Markov model analysis of single-molecule trajectories.
This project provides tools for estimating the number of metastable states, rate
constants between the states, equilibrium populations, distributions
characterizing the states, and distributions of these quantities from
sing... | bhmm/bhmm | setup.py | Python | lgpl-3.0 | 5,358 | [
"Gaussian"
] | c63723120319018d54e3c17fda31f37d555f86123df81a787f5ec6aaeda5ed73 |
#!/usr/bin/env python
# coding: utf-8
#
# Copyright (C) 2013-2015 DNAnexus, Inc.
#
# This file is part of dx-toolkit (DNAnexus platform client libraries).
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may not
# use this file except in compliance with the License. You may obtain a copy
# ... | andyshinn/dx-toolkit | src/python/dxpy/scripts/dx.py | Python | apache-2.0 | 245,324 | [
"BWA"
] | 55211f24834520f871836ebfc9beb1455d7d71ef4aaeeac9e7b07ecd89aafaa1 |
########################################################################
# $HeadURL$
########################################################################
""" PieGraph represents a pie graph
The DIRAC Graphs package is derived from the GraphTool plotting package of the
CMS/Phedex Project by ... <to be ... | sposs/DIRAC | Core/Utilities/Graphs/PieGraph.py | Python | gpl-3.0 | 5,528 | [
"DIRAC"
] | 75adbc95de466f1ff3fbf4de0d8afdde0a0cfb0e35574ce8ec11af2eecd608c1 |
import struct
import array
import string
import numpy
import datetime
from netCDF4 import Dataset
from os import listdir
from os import system
import os.path
import os
user = os.environ['USER']
lock_fname = 'lock_tower_merge_for_{}'.format(user)
if os.path.isfile(lock_fname):
print('ERROR: ... | zrick/tlab | scripts/python/tower2nc.py | Python | gpl-3.0 | 12,284 | [
"NetCDF"
] | 8d7145aebd8460a46c452b8a900f69a128f59466a38bc323e474da4f7a224f3e |
## INFO ########################################################################
## ##
## formbuilder ##
## =========== ... | petervaro/formbuilder | formdict.py | Python | gpl-3.0 | 3,166 | [
"VisIt"
] | 60ed60e8b7832db9f090d3201ad68ef69953ba67a7b4258ff9924d203fb973ba |
import numpy as np
import numpy.linalg as la
class Kernel(object):
"""Implements list of kernels from
http://en.wikipedia.org/wiki/Support_vector_machine
"""
@staticmethod
def linear():
return lambda x, y: np.inner(x, y)
@staticmethod
def gaussian(sigma):
return lambda x, ... | zhoucen/ml | Kernel.py | Python | mit | 897 | [
"Gaussian"
] | c1c9375e9dad55852b172be0a6cca7fa4fb4169a200bec0f29073403e3b11c98 |
"""
This module hears to welcome messages. Use it as a example.
"""
class WelcomeMessage:
def __init__(self, bot):
self.bot = bot
self.words = ['hello', 'hi', 'hola', 'que ase', 'que pasa', 'buenas']
def listenTo(self, channel, message, event):
return any([word in message.lower() for... | jonthebeach/estimator-bot | src/messages/welcome_message.py | Python | mit | 521 | [
"ASE"
] | 0ea87b309d3240ea25e83fbab320f02d7c0ca1a0093797f4fcd08018e6747934 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
This module provides a class to sample data along an elliptical path.
"""
import copy
import numpy as np
from .geometry import EllipseGeometry
from .integrator import INTEGRATORS
__all__ = ['EllipseSample']
class EllipseSample:
"""
Class ... | astropy/photutils | photutils/isophote/sample.py | Python | bsd-3-clause | 16,048 | [
"Galaxy"
] | 9504f506c127704df6d11860246fce7811817469e40f98ab987dd9cdc9217456 |
#!/usr/bin/python
#=============================================================================================
# Test MBAR by performing statistical tests on a set of of 1D harmonic oscillators, for which
# the true free energy differences can be computed analytically.
#
# A number of replications of an experiment i... | choderalab/pymbar | examples/harmonic-oscillators/harmonic-oscillators.py | Python | mit | 33,579 | [
"Gaussian"
] | 1431f1bd479ff02ce1a06e7b3b51f1561ca05d2a31c7a98b5221172543321398 |
#!/usr/bin/python3
########################################################################
# #
# Cyprium is a multifunction cryptographic, steganographic and #
# cryptanalysis tool developped by members of The Hackademy. #
# Fren... | underloki/Cyprium | kernel/crypto/text/octopus.py | Python | gpl-3.0 | 12,134 | [
"Octopus"
] | eef7a64a32c93960828a1f6e427452f8bc6c706a958a5c3674ffc711190c813d |
"""
network.py
Defines Network class which contains cell objects and network-realated methods
Contributors: salvadordura@gmail.com
"""
from __future__ import print_function
from __future__ import unicode_literals
from __future__ import division
from __future__ import absolute_import
from future import standard_lib... | thekerrlab/netpyne | netpyne/network/network.py | Python | mit | 5,784 | [
"NEURON"
] | cc1cae87dc8c05f4bc6cd6590fa3a2536d5945d29e21e0953b7e0aecb1da3019 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | Stargrazer82301/CAAPR | CAAPR/CAAPR_AstroMagic/PTS/pts/do/magic/prepare_image.py | Python | mit | 8,194 | [
"Galaxy"
] | 6105489e51541a42a8dd5ac6894d10676332d9297ae3e5ab216b74a9878045ef |
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