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# 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... | aam-at/tensorflow | tensorflow/python/ops/image_ops_impl.py | Python | apache-2.0 | 218,908 | [
"Gaussian"
] | 9e0b67df9b12b8a10d54df1267c6cbc66c11f3379e7a024965bcaa2033277985 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
# Copyright (C) 2011 Tim G L Lyons
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Publ... | arunkgupta/gramps | gramps/gen/filters/rules/citation/_hasgallery.py | Python | gpl-2.0 | 1,791 | [
"Brian"
] | afb8e3ede837b265e98e45051f1caf6d949cc8e64e120d0e9012efc89bcd3d06 |
#!/usr/bin/env python
"""
Retrieve a PDB file from the RCSB, solvate it, and minimize.
"""
################################################################################
# IMPORTS
################################################################################
try:
import openmm
from openmm import unit
... | choderalab/openmmtools | openmmtools/data/src-implicit/prepare_pdb.py | Python | mit | 4,208 | [
"CRYSTAL",
"OpenMM"
] | af6bf2ed2b7cd122dbcb09c31f03dc45a08c7f9a3c35b644a9e7fdd51df2e48a |
# !usr/bin/env python2
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2017-06-10 16:46:40
# @Last modified by: Brian Cherinka
# @Last Modified time: 2018-07-19 11:18:58
from __future__ import absolute_import, division, print_function
import os
from invoke ... | albireox/marvin | tasks.py | Python | bsd-3-clause | 6,373 | [
"Brian"
] | 23db0f3134c43207a27e96ac49036bd93c086acd82c6867e431aaed699ff1c08 |
from typing import Any, Dict
EMOJI_NAME_MAPS: Dict[str, Dict[str, Any]] = {
# seems like best emoji for happy
"1f600": {"canonical_name": "grinning", "aliases": ["happy"]},
"1f603": {"canonical_name": "smiley", "aliases": []},
# the Google emoji for this is not great, so made People/9 'smile' and
#... | punchagan/zulip | tools/setup/emoji/emoji_names.py | Python | apache-2.0 | 95,618 | [
"CRYSTAL",
"Octopus"
] | d64fad736e0f9c468924cd15cfa4476e28dbf369fc5a2a7287074b299d790eeb |
# vim: tabstop=4 shiftwidth=4 softtabstop=4
# Copyright (c) 2012 OpenStack, LLC.
# 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... | paulmathews/nova | nova/tests/compute/test_resource_tracker.py | Python | apache-2.0 | 24,202 | [
"exciting"
] | 2c0d4c8c28b5d51a0f2c906860c3b8ba06486763097a815bd52bb6f49d961803 |
from collections import ChainMap
import pytest
from context import RESOURCES, XTB_OPTIONS
from rdkit import Chem
from ppqm import chembridge, tasks, xtb
TEST_ENERGIES = [
("O", -5.0705443306),
("CC", -7.336370430847),
("[NH4+]", -4.615767064363),
]
TEST_SMILES = ["O", "N"]
def _get_options(tmpdir):
... | ppqm/ppqm | tests/test_xtb.py | Python | mit | 12,459 | [
"RDKit",
"xTB"
] | bc7748d9d0899788e06a63a8f09192cbda9c99beb07a8259390db6e177ea2a6c |
# -*- coding: utf-8 -*-
'''knife mixins'''
from threading import local
class CmpMixin(local):
'''
comparing knife mixin
'''
def all(self):
'''
Discover if :meth:`worker` is :const:`True` for **every** incoming
thing.
:rtype: :const:`self` (:obj:`knife` object)
... | lcrees/knife | knife/mixins.py | Python | bsd-3-clause | 28,874 | [
"MOE"
] | 49f493770d2c5aac6b675f68f0770ef10eefbf01eb4417be6ca191881bc03f2a |
# -*- coding: utf-8 -*-
# test_function.py ---
#
# Filename: test_function.py
# Description:
# Author: subha
# Maintainer:
# Created: Sat Mar 28 19:34:20 2015 (-0400)
# Version:
# Last-Updated:
# By:
# Update #: 0
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change log:
#
#
#
#
# This... | dharmasam9/moose-core | tests/python/test_function.py | Python | gpl-3.0 | 2,726 | [
"MOOSE"
] | f135f2ad0a116eb2241ca769c489949d36a54224ac75d9ef9eb077b74d2fe168 |
from ase import *
from numpy import random, pi
from box import Atoms
from box import mix
from hotbit import Hotbit
#from hotbit import Calculator0
from ase.units import Bohr, Hartree
from hotbit.test.misc import default_param
# C-non-SCC
calc=Hotbit(SCC=False,txt='test.cal',**default_param)
C=Atoms('C',positions=[(0,0... | pekkosk/hotbit | hotbit/test/atom_dimer.py | Python | gpl-2.0 | 1,382 | [
"ASE"
] | b34fc804691328abf71db79ebf082fac9cda13734d6d7b8d44a7ad48d0816732 |
#! /usr/bin/env python
import argparse
import Model
import os
import itertools
import pdb
import re
def uniq(seq):
seen = set()
seen_add = seen.add
return [ x for x in seq if not (x in seen or seen_add(x))]
MODELS = ["EC-EARTH3",
"EC-EARTH3-WAM",
"MPIESM_1_1",
"MPIESM_1_no_e... | marev711/scripts | drs-list-variables/list-drs-data-files.py | Python | mit | 4,777 | [
"NetCDF"
] | 848c246c3b37a20b3726d5937fd8b62e2b07dc81c278bafd65e9f9c1c1e592f0 |
"""separate.py
this module is part of the ciderseq distribution.
"""
import os
import uuid
import tempfile
from Bio import SeqIO
from Bio.Blast.Applications import NcbiblastnCommandline
from Bio.Blast import NCBIXML
def separate(settings,seq,logger):
logger.debug("separate > "+str(seq.id))
#define return variable... | hirschhm/ciderseq | cider/separate.py | Python | agpl-3.0 | 1,694 | [
"BLAST"
] | aa74967ad05ca977e4e603b03e969586e53ca90f10e82a2498456a300b8345c5 |
#!/usr/bin/env python
from nutils import *
from . import register, unittest
import scipy.special, re
@register( 'line', 1, True )
@register( 'quad', 2, True )
@register( 'hex', 3, True )
@register( 'tri', 2, False )
@register( 'tet', 3, False, maxdegree=8 )
def gauss( ndims, istensor, maxdegree=7, eps=1e-12 ):
# G... | timovanopstal/nutils | tests/quadrature.py | Python | mit | 14,063 | [
"Gaussian"
] | 891331d3a8d832b3d76c93dc515d2c0eec96b9183fd75c7267775ec60a52be11 |
import weakref
import ast
import re
from uxie.utils import idle, join_to_file_dir, refresh_gui
from uxie.misc import BuilderAware
from snaked.util import set_activate_the_one_item
match_ws = re.compile('^[ \t]+')
def get_ws_len(line):
match = match_ws.search(line)
if match:
return len(match.group(0))... | baverman/snaked | snaked/plugins/python/outline.py | Python | mit | 5,288 | [
"VisIt"
] | 53bc86b7073374f3968fb139c0ae523e186d19bc95022c7407269d19f750ab1e |
# neareast positive semi-definite matrix algorithm from Higham (2000)
# This is used to ensure that the covariance matrice estimates obtained from the
# kmeans segmentation clustering are positive definite. This is a requirement
# for multivariate gaussian density function (well positive semi-definite but this
# woul... | arthurfait/HMM-3 | hmm/nearPD_Higham.py | Python | gpl-3.0 | 1,212 | [
"Gaussian"
] | b983b652a620ac506e035a14dee867cf19be1832a58040d7e54e45b85e650168 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
chose m, c (parameters) for a straight line
from the line pick N points (N=3, 5, 50, 100, 1000)
pick sigma (size of the noise)
randomly deviate(offset) points in y direction by using
sigma*random number from normal distribution
sigma the same for all points
then defin... | lefthandedroo/Cosmo-models | History/Stats/emcee_ex_3.py | Python | mit | 6,897 | [
"Gaussian"
] | 69620a9f69ae2462a701acb42dc1d3d1d564981b56545b1f284c953033f3870a |
"""HTSeq is a package to process high-throughput sequencing data.
See htseq.readthedocs.io/en/master/index.html for documentation.
"""
import itertools
import warnings
import os
import shlex
import sys
from _HTSeq import *
from _version import __version__
#########################
# Utils
#########################... | simon-anders/htseq | python2/HTSeq/__init__.py | Python | gpl-3.0 | 44,210 | [
"Bowtie",
"HTSeq",
"pysam"
] | 7c860d37b35be7e47e48a457ef6ac9715eb6fd41b886713d2be8cf0c1d5ced6d |
import sys
import time
from pysisyphus.calculators.Calculator import Calculator
from pysisyphus.calculators import ORCA, XTB, ORCA5
CALC_CLASSES = {
"orca": ORCA.ORCA,
"orca5": ORCA5.ORCA5,
"xtb": XTB.XTB,
}
try:
from pysisyphus.calculators import PySCF
CALC_CLASSES["pyscf"] = PySCF.PySCF
except... | eljost/pysisyphus | pysisyphus/calculators/MultiCalc.py | Python | gpl-3.0 | 2,276 | [
"ORCA",
"PySCF",
"xTB"
] | 53dd271089b35eafc34502a529c2953aac59fec3ad5231982110198c98bb085f |
# Import the WSRC module that provides all of the code
# to run a waterswap simulation
from Sire.Tools import WSRC
# Import the Units module so that we can specify the dimensions
# (units) of input parameters
from Sire.Units import *
# Import the Stream module so that we can save restart files
import Sire.Stream
# ... | chryswoods/SireTests | examples/wsrc/runwsrc.py | Python | gpl-2.0 | 2,399 | [
"Amber"
] | 5083596d5a845df72b99d7a93ff14dae11d10d89db5eb0c8b7c6d92cc8e89d9b |
# NOTE: This example uses the next generation Twilio helper library - for more
# information on how to download and install this version, visit
# https://www.twilio.com/docs/libraries/python
from twilio.rest import Client
# Your Account Sid and Auth Token from twilio.com/user/account
account = "ACXXXXXXXXXXXXXXXXXXXXX... | teoreteetik/api-snippets | notifications/rest/notifications/send-notification/send-notification.6.x.py | Python | mit | 556 | [
"VisIt"
] | 24d3f29036aa966f1b527b76d4e38a5b73ac21710caef3345e21059d7f12bffe |
#!/usr/local/bin/env python
"""
Test repex.py facility.
TODO
* Create a few simulation objects on simple systems (e.g. harmonic oscillators?) and run multiple tests on each object?
"""
#=============================================================================================
# GLOBAL IMPORTS
#=================... | choderalab/brokenyank | tests/test_repex.py | Python | lgpl-3.0 | 19,149 | [
"NetCDF",
"OpenMM"
] | c7e002d3fa6c61a18c64e4b867211b4b899b92064e7d5528b183e001eaef860b |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
import logging
import math
import itertools
import warnings
from collections import OrderedDict
import numpy as np
from matplotlib import patch... | xhqu1981/pymatgen | pymatgen/electronic_structure/plotter.py | Python | mit | 161,089 | [
"BoltzTrap",
"Gaussian",
"Mayavi",
"VASP",
"pymatgen"
] | 440cfa8124980b04dd9186a9b8bf54b557719b8c6ba92dc596c945cff957b8ab |
"""
Bayesian hidden Markov models.
"""
import numpy as np
import copy
import time
#from scipy.misc import logsumexp
import bhmm.hidden as hidden
from bhmm.msm.tmatrix_disconnected import sample_P
from bhmm.util.logger import logger
from bhmm.util import config
#from bhmm.msm.transition_matrix_sampling_rev import Tra... | jchodera/bhmm-force-spectroscopy-manuscript | bhmm/estimators/bayesian_sampling.py | Python | lgpl-3.0 | 9,311 | [
"Gaussian"
] | 546c18f30ab33c4a682f97707f2227e29278a18d3597a71c4fe41da85c5460d0 |
import random
import matplotlib.pyplot as plt
def summation(result,first):
array = []
third = result - first
first = (16 + first)/96 #first character
third = (16 + third)/96 #third character
second = 11/96 #this correspond to the character '+'
array.append(first)
array.append(seco... | LorenzoM1997/math-neural-network | math_neural_network_0.0.5.py | Python | mit | 5,260 | [
"NEURON"
] | e04ddb6d89775e95afa431300bd3b57d1fce035df94148f5c8a205d71ce2d18c |
# -*- coding: utf-8 -*-
##
## This file is part of CDS Invenio.
## Copyright (C) 2002, 2003, 2004, 2005, 2006, 2007, 2008 CERN.
##
## CDS Invenio is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## published by the Free Software Foundation; either versio... | lbjay/cds-invenio | modules/websubmit/lib/websubmitadmin_engine.py | Python | gpl-2.0 | 245,642 | [
"VisIt"
] | bba6d56678af202235e72f48466750aa4098945284697e78c16e9c4e2405fc03 |
# (c) 2012, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any lat... | Shaps/ansible | lib/ansible/template/safe_eval.py | Python | gpl-3.0 | 5,360 | [
"VisIt"
] | 694b1ee761c8993abae2581e88273a6fcab9ec8610d39ae2b60666f0cb1bdebb |
#Python 2.7.9 (default, Apr 5 2015, 22:21:35)
# the full environment I've tested this in is in basic_project_stats.yml
# note: this code replicates a lot of what's in basic_project_stats.py
# and then builds on it.
'''
sessions_inproj_byuser:
Computes session statistics for each user who has classified on your proj... | plorch/FocusOnWildlifeCMPScripts | sessions_inproj_byuser.py | Python | gpl-2.0 | 28,167 | [
"Galaxy"
] | d7fcdc0e8b2588d60b8d600b74b7807aff2c36fa4682104ffe45b6fa2abf9e6a |
#
# A file that opens the neuroConstruct project LarkumEtAl2009 and run multiple simulations stimulating ech terminal apical branch with varying number of synapses.
#
# Author: Matteo Farinella
from sys import *
from java.io import File
from java.lang import System
from java.util import ArrayList
from uc... | pgleeson/TestArea | models/LarkumEtAl2009/pythonScripts/PAP_multibranches_inhibition.py | Python | gpl-2.0 | 22,104 | [
"NEURON"
] | 1c28b63a0c2cec0c9828cf9dd57ca573000b36de0160114454f705396a54172a |
#!/usr/bin/env python
"""
Demo pipeline for processing voltage imaging data. The processing pipeline
includes motion correction, memory mapping, segmentation, denoising and source
extraction. The demo shows how to construct the params, MotionCorrect and VOLPY
objects and call the relevant functions. See inside for det... | agiovann/Constrained_NMF | demos/general/demo_pipeline_voltage_imaging.py | Python | gpl-2.0 | 9,880 | [
"Gaussian"
] | 75e30191addb551223b0e0601a1de22c67841c2ed135b7bb4af2fa629728c4b1 |
#------------------------------------------------------------------------------
# pycparser: c_generator.py
#
# C code generator from pycparser AST nodes.
#
# Copyright (C) 2008-2012, Eli Bendersky
# License: BSD
#------------------------------------------------------------------------------
from . import c_ast
class... | imjonsnooow/vivisect | vivisect/contrib/pycparser/pycparser/c_generator.py | Python | apache-2.0 | 13,860 | [
"VisIt"
] | f27ce74ddb015727f25c35b63f7faeec275180cabcc4efe4706f44a6ad0211a2 |
from docutils.nodes import figure, caption, Text, reference, raw, SkipNode, Element
from sphinx.roles import XRefRole
# Element classes
class page_ref(reference):
pass
class num_ref(reference):
pass
# Visit/depart functions
def skip_page_ref(self, node):
raise SkipNode
def latex_visit_page_ref(self,... | ProteinDF/ProteinDF_userman | source/exts/numfig.py | Python | gpl-3.0 | 3,182 | [
"VisIt"
] | bb13932d3270d497ba97426afc42e369dae118b9a9f6c13dcdc0b0e1d9f3485f |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | ashutoshvt/psi4 | psi4/driver/p4util/fcidump.py | Python | lgpl-3.0 | 17,523 | [
"Psi4"
] | c5f424b863841baeb69f5bc56981fbca72f0c064b5058bac174ee83c6e68903f |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Mon Apr 17 12:41:17 2017
@author: kostenko
Simulate makes fake polychromatic x-ray CT data
"""
#import tomopy.misc
#import tomo_wrap as tw
#import xraydb
class spectra():
'''
Simulates spectral phenomena that involve x-ray-matter interaction
... | cicwi/seashell_project | simulate.py | Python | mit | 4,458 | [
"Gaussian"
] | 597197a57fb79ae202de0bce26f63dfd7561d6a226d93c03a4a59115046e6797 |
#!/usr/bin/env python
# * 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/licen... | nuclear-wizard/moose | scripts/verify_conda_libmesh.py | Python | lgpl-2.1 | 3,457 | [
"MOOSE"
] | 5782839e7307b78c9e98004075430004c2ca9ddf9ae2cbe9a68952cc55b89dd1 |
from tools.load import LoadMatrix
from sg import sg
from numpy import *
num=100
labelstrain=concatenate((-ones([1,num]), ones([1,num])),1)[0]
featuretrain=concatenate((random.normal(size=(2,num))-1,random.normal(size=(2,num))+1),1)
parameter_list=[[1.,labelstrain,featuretrain,1e-2],
[1.,labelstrain,feat... | chenmoshushi/shogun | examples/undocumented/python_static/mkl_regression.py | Python | gpl-3.0 | 1,073 | [
"Gaussian"
] | adaa602111bd849481f35bc91bdf8c10497362ae26a0e5736f164c9d26e47c7f |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
from monty.os.path import which
from monty.serialization import dumpfn, loadfn
from pymatgen.core.structure import Molecule
from pymatgen.io.qchem.outputs import QCOutput, check_for... | gmatteo/pymatgen | pymatgen/io/qchem/tests/test_outputs.py | Python | mit | 9,535 | [
"pymatgen"
] | 8e775768857e454ab46617749a2f18d370758573a4f2499dd1828598ae061499 |
# -*- coding: utf-8 -*-
import copy
from collections import namedtuple
import re
from . import exceptions
HKL = namedtuple('HKL', ('h', 'k', 'l'))
def hkl_to_tuple(hkl_input):
"""If hkl_input is a string, extract the hkl values and
return them as (h, k, l). If hkl_string is not a string, return it
unmo... | m3wolf/scimap | scimap/reflection.py | Python | gpl-3.0 | 2,867 | [
"CRYSTAL"
] | d5e9334265646948159b25f09939249f7159b15f4f4ae41beb5d7d1c195d067b |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | test/test_request_plan_find.py | Python | apache-2.0 | 10,031 | [
"VisIt"
] | c18a67847ba9f4e58b952d027d808e4d191f0e3eace9940bdd86047bbe962deb |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | gregcaporaso/scikit-bio | skbio/io/format/_base.py | Python | bsd-3-clause | 7,483 | [
"scikit-bio"
] | b067ebf4d4e42f193ce5dd1b72438051ae4b74aa38aeedb3bec74bbe74cc8ec7 |
import logging
import simplejson
import time
import tempfile
from dirac.lib.base import *
from pylons.controllers.util import redirect_to
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities import List, Time, DEncode
from dirac.lib.credentials import authorizeAction
from dirac.lib.diset import getRPCCli... | DIRACGrid/DIRACWeb | dirac/controllers/systems/activitiesMonitoring.py | Python | gpl-3.0 | 10,443 | [
"DIRAC"
] | fd359546ae645c343f33a1b504ac07ebeff90b7e8a07326487e02d57bac6f5e4 |
"""
Linter classes containing logic for checking various filetypes.
"""
import ast
import io
import os
import re
import textwrap
from xsslint import visitors
from xsslint.reporting import ExpressionRuleViolation, FileResults, RuleViolation
from xsslint.rules import RuleSet
from xsslint.utils import Expression, Parse... | eduNEXT/edx-platform | scripts/xsslint/xsslint/linters.py | Python | agpl-3.0 | 66,920 | [
"VisIt"
] | d71b412257b5dc190207a82a7f5bade23e3b5eb911a495543b3ce8f387a60bac |
"""Read and write notebooks in JSON format.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is in
# the file COPYING, distribute... | noslenfa/tdjangorest | uw/lib/python2.7/site-packages/IPython/nbformat/v3/nbjson.py | Python | apache-2.0 | 2,035 | [
"Brian"
] | aea47cb31e1261527eea86ed1eb787c9f8ccf532d9d3a0294834225950471d63 |
"""Sensitive variant calling using VarDict.
Defaults to using the faster, equally sensitive Java port:
https://github.com/AstraZeneca-NGS/VarDictJava
if 'vardict' or 'vardict-java' is specified in the configuration. To use the
VarDict perl version:
https://github.com/AstraZeneca-NGS/VarDict
specify 'vardict-perl'.... | a113n/bcbio-nextgen | bcbio/variation/vardict.py | Python | mit | 19,572 | [
"BWA"
] | 56230f84b54e75b53622da5c33f63bd7063dd74b3efc782b97de43bb1e231b35 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | manuzhang/beam | sdks/python/apache_beam/transforms/ptransform.py | Python | apache-2.0 | 25,553 | [
"VisIt"
] | 086d3060e6a63241edaac7009dbf8e537a86744cf9dc4dcb3d7dcbb4dca1c59b |
'''
input: a data object
as returned by GeostationaryFactory.create_scene(sat, str(sat_nr).zfill(2), "seviri", time_slot)
or by global_data.project(area, precompute=True)
output:
image function according to the input string
'''
from __future__ import division
from __future__ import print_function
import products... | meteoswiss-mdr/monti-pytroll | scripts/my_msg_module.py | Python | lgpl-3.0 | 53,704 | [
"DIRAC",
"NetCDF"
] | 56a9f34d0927f07e4aa900c62d1765059512de13afbd91bb7a46900a8d93389c |
import os
import pysam
import unittest
from TestUtils import checkFieldEqual
import copy
SAMTOOLS = "samtools"
WORKDIR = "pysam_test_work"
DATADIR = "pysam_data"
class ReadTest(unittest.TestCase):
def buildRead(self):
'''build an example read.'''
a = pysam.AlignedSegment()
a.query_name ... | dannon/pysam | tests/AlignedSegment_test.py | Python | mit | 20,563 | [
"pysam"
] | 23d730d2254ab9f2179615b288a7564b784ad510cb5e33f6ef659119405d49fe |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from bowtie.visual import Plotly, SmartGrid
from bowtie.control import Slider, Number, Button
from bowtie import cache, command, Pager
import numpy as np
import plotlywrapper as pw
import plotly.graph_objs as go
pager = Pager()
#
# Initialize our values
#
# This prevents ... | rsm5139/learning-bowtie | step_2.py | Python | mit | 4,535 | [
"Bowtie"
] | 48f63e85319bb05422de60dca3be561badbd5bace6a4e1b21d2e611972c3d041 |
class VehicleInfo(object):
def __init__(self):
"""
make_target: option passed to make to create binaries. Usually sitl, and "-debug" may be appended if -D is passed to sim_vehicle.py
default_params_filename: filename of default parameters file. Taken to be relative to autotest dir.
... | cast051/ardupilot_cast | Tools/autotest/pysim/vehicleinfo.py | Python | gpl-3.0 | 10,835 | [
"Firefly"
] | 5ce859eb9edfa244a001cef872e2522afa0f754ec51040a572027827b0c5d699 |
# vizmdend setup.py
from distutils.core import setup
setup(
name = 'vizmdend',
packages = ['vizmdend','vizmdend/test' ],
version = '1.1.0',
description = 'AMBER mdend file inspector',
author = 'Jose Borreguero',
author_email = 'jose@borreguero.com',
url = 'https://github.com/camm-sns/vizmd... | camm/vizmdend | setup.py | Python | mit | 866 | [
"Amber"
] | 4a9ef2de1a606881cfa9801ee98501e5c24cdbce5e4e89446252727bb5264809 |
#!/usr/bin/env python3
#
# Copyright (C) 2013-2017(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, e... | espressopp/espressopp | testsuite/rattle/testRattle.py | Python | gpl-3.0 | 4,973 | [
"ESPResSo"
] | 3e8ffd84bf4d35c651dbd0e1a6c70ca92d749e296eab909770f052e8ae10d72e |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2015 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 General Public License as published by
## the Free Software Foundati... | andrebellafronte/stoq | stoqlib/gui/test/test_stockdecreaseeditor.py | Python | gpl-2.0 | 4,992 | [
"VisIt"
] | 73abef4df612d442fc12921c8886b20a4c2135c206a72ec0f42b546ebf21b370 |
#!/usr/bin/env python
#
# Copyright (c) 2011-2013 by California Institute of Technology
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the abov... | pombredanne/nTLP | benchmark/benchmark_tools.py | Python | bsd-3-clause | 18,830 | [
"VisIt"
] | 4cc4c63acd5236d33ef126174adb7fab36f734a0f840dd118240f7880a28546f |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
from datetime import datetime, timedelta
from flaky import flaky
from textwrap import dedent
from unittest import skip
from nose.plugins.attrib import attr
import pytz
import urllib
from bok_choy.promise import EmptyPromise
from common.test.acceptance.tests... | romain-li/edx-platform | common/test/acceptance/tests/lms/test_lms.py | Python | agpl-3.0 | 58,905 | [
"VisIt"
] | 7fe5c7637eb2651563e2e0ff49c7582a431ada55f4b286f639c74c122a0de78e |
#!/usr/bin/env python
########################################
#Globale Karte fuer tests
# from Rabea Amther
########################################
# http://gfesuite.noaa.gov/developer/netCDFPythonInterface.html
import math
import numpy as np
import pylab as pl
import Scientific.IO.NetCDF as IO
import matplotlib as ... | CopyChat/Plotting | GCM_changes/bias.TCC.GCMs.py | Python | gpl-3.0 | 4,972 | [
"NetCDF"
] | ee7544c758ce537d532bbdd69544d34ed9c159854ce04dadc260b95160a1131d |
#pylint: disable=W0403,C0103,R0901,R0904,R0913,C0302
from __future__ import (absolute_import, division, print_function)
from six.moves import range
import numpy
import sys
from HFIR_4Circle_Reduction import fourcircle_utility
from HFIR_4Circle_Reduction import guiutility
import HFIR_4Circle_Reduction.NTableWidget as t... | wdzhou/mantid | scripts/HFIR_4Circle_Reduction/hfctables.py | Python | gpl-3.0 | 55,218 | [
"Gaussian"
] | d7da3a8e1c7cc3d08ac4e211ebd31a23285cc74de0b54673c60f65fd699e4bd6 |
# file findingaids/content/forms.py
#
# Copyright 2012 Emory University Library
#
# 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... | mprefer/findingaids | findingaids/content/forms.py | Python | apache-2.0 | 6,521 | [
"VisIt"
] | 816080db1d7b7b38c890b9792e6f1c9ebfffe96e8b0cc3cfc377f8eb93d97c49 |
"""
fillerbase Module
Classes to help fill widgets with data
Copyright (c) 2008 Christopher Perkins
Original Version by Christopher Perkins 2008
Released under MIT license.
"""
from configbase import ConfigBase, ConfigBaseError
from metadata import FieldsMetadata
from genshi import XML
import inspect
from datetime i... | jokajak/itweb | data/env/lib/python2.6/site-packages/sprox-0.6.10-py2.6.egg/sprox/fillerbase.py | Python | gpl-3.0 | 11,370 | [
"VisIt"
] | 8c3ee6eac3317e83b279a8801582e99084a74daec85a8218c48987b84124b640 |
# -*- coding: utf-8 -*-
# Copyright 2012 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless require... | harshilasu/GraphicMelon | y/google-cloud-sdk/platform/gsutil/gslib/addlhelp/support.py | Python | gpl-3.0 | 4,066 | [
"VisIt"
] | cba9099246b4e8c9036130446b01ffa6f1bc5e0a4520dc4d0c7ac09fab0fd06c |
import numpy as np
import matplotlib.pyplot as plt
import sys
from vayu import block
from vayu.block.monitor import monitor
from vayu.block.meshbase import Mesh
from vayu.block.topology import MeshParse
import vayu.block.util as util
from vayu.solver import euler
from vayu.solver.euler_constants import *
from vayu.blo... | henrynj/PMLMC | v0.0/model_euler_ls89.py | Python | gpl-3.0 | 8,558 | [
"Gaussian"
] | 12cff4e05f75282810958c74ce6170103b14cf4e06e0e13f33bb110e2432e573 |
# coding=utf-8
from setuptools import setup
with open('requirements.txt') as f:
requirements = f.read().splitlines()
setup(name='Amber',
version='0.1.1',
description='Text Adventure interpreter',
classifiers=[
'Development Status :: 4 - Beta',
'License :: OSI Approved :: MIT ... | DefaltSimon/Amber | setup.py | Python | mit | 669 | [
"Amber"
] | 939e7e7826ae4be718dc4066175c55783cfca5232801cea9a2ee7578aa98ea8b |
""" :mod: ProcessPoolTests
=======================
.. module: ProcessPoolTests
:synopsis: unit tests for ProcessPool
.. moduleauthor:: Krzysztof.Ciba@NOSPAMgmail.com
unit tests for ProcessPool
"""
import os
import sys
import random
import time
import threading
import pytest
from DIRAC import gLogger
from ... | DIRACGrid/DIRAC | src/DIRAC/Core/Utilities/test/Test_ProcessPool.py | Python | gpl-3.0 | 10,996 | [
"DIRAC"
] | 27396c53d1f1e67cbf237739fca630a769f15d74071079d41dfda8f6e03dd78d |
"""
Physical units and dimensions.
The base class is Unit, where all here defined units (~200) inherit from.
The find_unit function can help you find units for a given quantity:
>>> import sympy.physics.units as u
>>> u.find_unit('coul')
['coulomb', 'coulombs']
>>> u.find_unit(u.charge)
['C', 'ch... | drufat/sympy | sympy/physics/units.py | Python | bsd-3-clause | 8,849 | [
"Avogadro"
] | b25e07e7344de24695cc6a5cbd3831710678942b43c7aa7199cbdb4f743c0d8d |
# -*- 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-texttospeech | tests/unit/gapic/texttospeech_v1beta1/test_text_to_speech.py | Python | apache-2.0 | 60,376 | [
"Octopus"
] | 67f700e779179fdb350aeac88b5922e1c7d214977b096e1e0e58dcc6b3a8626a |
# -*- coding: utf-8 -*-
# This code is part of Amoco
# Copyright (C) 2018 Axel Tillequin (bdcht3@gmail.com)
# published under GPLv2 license
# spec_xxx files are providers for instruction objects.
# These objects are wrapped and created by disasm.py.
from amoco.logger import Log
logger = Log(__name__)
logger.debug("... | bdcht/amoco | amoco/arch/v850/spec_v850e2s.py | Python | gpl-2.0 | 17,655 | [
"ADF"
] | 830adaf318a029d259d3f16a936fe7d791aab7f64a869646caa904de86d7c2a2 |
# -*- coding: utf-8 -*-
import os
import random
def count(w1, wnew):
return sum(c1 == c2 for c1, c2 in zip(w1, wnew))
def best_shuffle(w):
wnew = list(w)
n = len(w)
rangelists = (list(range(n)), list(range(n)))
for r in rangelists:
random.shuffle(r)
rangei, rangej = rangelists
... | NicovincX2/Python-3.5 | Algorithmique/Mathématiques discrètes/Combinatoire/Permutation aléatoire/shuffle.py | Python | gpl-3.0 | 939 | [
"Elk"
] | 320c5176d1d973f56828ea3059c496f150e529f675b223df85f4257ef8f60e88 |
# -*- coding: utf-8 -*-
#
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
#... | adamhaney/airflow | tests/plugins/test_plugin.py | Python | apache-2.0 | 3,908 | [
"Galaxy"
] | 22319b142dee11ab5b7b095f85dc2adef60ddd8c172a07b1470cd88cf2a7587b |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The fsl module provides classes for interfacing with the `FSL
<http://www.fmrib.ox.ac.uk/fsl/index.html>`_ command line tools. This
was written to work with FSL version 4.1.4.
Change directory to p... | iglpdc/nipype | nipype/interfaces/fsl/preprocess.py | Python | bsd-3-clause | 75,808 | [
"Gaussian",
"VTK"
] | 2d42ae478ec5626350a0f7b4216918bd44a9cd90a01a295a8cfd04bc787e7a7a |
# -*- coding: utf-8 -*-
"""
Regression tests for the Test Client, especially the customized assertions.
"""
import os
from django.conf import settings
from django.test import Client, TestCase
from django.test.utils import ContextList
from django.core.urlresolvers import reverse
from django.core.exceptions import Suspi... | faun/django_test | tests/regressiontests/test_client_regress/models.py | Python | bsd-3-clause | 42,064 | [
"VisIt"
] | fd33c76f920e757e8c7885c1703555880850b36ee497784cd4c1d1cf56ed728b |
"""
=====================
CollectionViewer demo
=====================
Demo of CollectionViewer for viewing collections of images. This demo uses
the different layers of the gaussian pyramid as image collection.
You can scroll through images with the slider, or you can interact with the
viewer using your keyboard:
le... | michaelpacer/scikit-image | viewer_examples/viewers/collection_viewer.py | Python | bsd-3-clause | 800 | [
"Gaussian"
] | deb3128ad462921e73691a72b0548f70a71353fbc65b7af66869d25e913e4ecd |
# (c) 2013-2016, Michael DeHaan <michael.dehaan@gmail.com>
# Stephen Fromm <sfromm@gmail.com>
# Brian Coca <briancoca+dev@gmail.com>
# Toshio Kuratomi <tkuratomi@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under t... | ravibhure/ansible | lib/ansible/plugins/action/assemble.py | Python | gpl-3.0 | 6,428 | [
"Brian"
] | a956996c0ab5cc74e4d53ad9d0cdec2698ca56b4a5367505f50ed6bcba6516fe |
# Copyright 2016, Ray1235
# CoDMayaTools 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 version.
#
# This program is distributed in the hope t... | Ray1235/CoDMayaTools | CoDMayaTools.py | Python | gpl-3.0 | 161,584 | [
"VisIt"
] | 550b51bba1d0fbe7d12041609aabc997ba33f917d5c4f4a894a1dc04d3712ea7 |
# The PGP Word List, which maps bytes to phonetically-distinct words. There
# are two lists, even and odd, and encodings should alternate between then to
# detect dropped words. https://en.wikipedia.org/wiki/PGP_Words
# Thanks to Warren Guy for transcribing them:
# https://github.com/warrenguy/javascript-pgp-word-lis... | shaunstanislaus/magic-wormhole | src/wormhole/wordlist.py | Python | mit | 9,117 | [
"ORCA"
] | b5ec40a1d79a4d83a832974e07eebab579ae9dbeaa95ac419575ef55585618be |
import random
from hearthstone.enums import CardClass, CardType, GameTag, PlayReq, Race, Rarity
from ..actions import *
from ..aura import Refresh
from ..dsl import *
from ..events import *
# For buffs which are removed when the card is moved to play (eg. cost buffs)
# This needs to be Summon, because of Summon fro... | jleclanche/fireplace | fireplace/cards/utils.py | Python | agpl-3.0 | 4,338 | [
"CRYSTAL"
] | fef164c034694e567af51214233035a4da3ae21a179060fb9b311b8e48c8a534 |
"""
@author: Alex Kerr
"""
import numpy as np
import kappa
amber = kappa.Amber(dihs=False, angles=True, lengths=True)
# create stubby cnt
cnt = kappa.build(amber, "cnt", radius=1, length=20)
#kappa.plot.bonds(cnt, indices=True)
#kappa.plot.faces(cnt)
indices = [2, 57]
for i in range(1,51):
# generate pol... | ajkerr0/kappa | tutorial/generate_lammps_files.py | Python | mit | 907 | [
"Amber"
] | e6790d4cf8cf7fe2f70feebaf0d4a3c5d6906001414b6207f1178030489ff524 |
#! /usr/bin/env python
# ==========================================================================
# This script performs an unbinned maximum likelihood analysis for a
# variety of models. This allows checking the models.
#
# Copyright (C) 2011-2012 Juergen Knoedlseder
#
# This program is free software: you can redist... | cdeil/ctools | test/example_models.py | Python | gpl-3.0 | 3,792 | [
"Gaussian"
] | 01c33e92f230dae5f098cbd06a487d569672c00514dac2de208e4638ef3b168e |
#!/usr/bin/env python
# File created on 09 Feb 2010
from __future__ import division
__author__ = "Antonio Gonzalez Pena"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Rob Knight", "Greg Caporaso", "Kyle Bittinger",
"Antonio Gonzalez Pena", "David Soergel", "Jose Antonio Navas Molin... | wasade/qiime | scripts/assign_taxonomy.py | Python | gpl-2.0 | 24,765 | [
"BLAST"
] | d49b286e0bc053b7ad970c6b8a5d927b693726d7eea7c9d948791626333ddf19 |
from bs4 import BeautifulSoup
import urllib
from scraper import *
import re, json
class Galaxy(Scraper):
def get_planets(self, galaxy, system):
"""
Get planets in the given galaxy and system
"""
self.logger.info('Getting data from system %s:%s' % (galaxy, system))
url = sel... | yosh778/OG-Bot | ogbot/scraping/galaxy.py | Python | mit | 3,833 | [
"Galaxy"
] | 2b1ba78b0c98d2c2b5d2d3a8b70381bf2cd78f16ee08887642e514f3ffe008b1 |
# -*- coding: utf-8 -*-
##############################################################################
#
# OpenERP, Open Source Management Solution
# Copyright (C) 2004-2010 Tiny SPRL (<http://tiny.be>).
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU... | crmccreary/openerp_server | openerp/addons/project/project.py | Python | agpl-3.0 | 61,446 | [
"VisIt"
] | 60c869c4245a67a1081c8d8898cad5d7994aa2f0c0e18973f7e887331922c744 |
# Copyright (C) 2015 Atsushi Togo
# All rights reserved.
#
# This file is part of phono3py.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must retain the above copyright
# noti... | atztogo/phono3py | phono3py/cui/settings.py | Python | bsd-3-clause | 32,490 | [
"phonopy"
] | aadb3085f972d0ee1c22595651ff5bd642002b4bd15ca626c246e6bd537dd57c |
#!/usr/bin/python
# gly21.py -- N-linked protein glycosylator (2017.5.31)
# 2016.10.05 -- first version -- John Saeger
# This version complains about incomplete sidechains. You must fix them up.
# I use pymol's mutate wizard to mutate a residue to itself.
# This version has a slightly more sophisticated solvent expo... | aequorea/gly | versions/gly21.py | Python | gpl-2.0 | 7,050 | [
"PyMOL"
] | 69f7a225a31b671885be2264e65b85930bbfc3c45d4dee3f658c442300b88b6d |
# Outdoor Solar Adjusted Temperature Calculator
#
# Ladybug: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Ladybug.
#
# Copyright (c) 2013-2015, Chris Mackey <Chris@MackeyArchitecture.com>
# Ladybug is free software; you can redistribute it and/or modify ... | boris-p/ladybug | src/Ladybug_Outdoor Solar Temperature Adjustor.py | Python | gpl-3.0 | 84,745 | [
"EPW"
] | 962b806a8719f35c3199cdad3f4be8dca73fb4d3d8157075a1d4a299d532365a |
r"""Metric space in which the Hamiltonian dynamic is embedded.
An important particular case (and the most used in practice) of metric for the
position space in the Euclidean metric. It is defined by a definite positive
matrix :math:`M` with fixed value so that the kinetic energy of the hamiltonian
dynamic is independe... | blackjax-devs/blackjax | blackjax/mcmc/metrics.py | Python | apache-2.0 | 5,595 | [
"Gaussian"
] | b3832dcff395f75849e23affcd9fb22555ab5fc354cfc012e0c39f854cfd26d4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""
Derive Beta Series Maps
^^^^^^^^^^^^^^^^^^^^^^^
.. autofunction:: init_betaseries_wf
"""
from __future__ import print_function, division, absolute_import, u... | HBClab/NiBetaSeries | src/nibetaseries/workflows/model.py | Python | mit | 11,580 | [
"Gaussian"
] | 2d0af8d7a47764057d7520361a0a695cae7863338d334b343e7646dacfeb7a91 |
import unittest
import numpy as np
from operator import itemgetter
from AlphaGo.go import GameState
from AlphaGo.mcts import MCTS, TreeNode
class TestTreeNode(unittest.TestCase):
def setUp(self):
self.gs = GameState()
self.node = TreeNode(None, 1.0)
def test_selection(self):
self.nod... | Rochester-NRT/AlphaGo | tests/test_mcts.py | Python | mit | 5,396 | [
"VisIt"
] | 575450b37178e1317d772b51bc4b3e8eb3019e2fab93fe116472bf632065b416 |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
#
# License: BSD (3-clause)
import numpy as np
import os
import os.path as op
from scipy import sparse, linalg
from copy import deepcopy
from .io.constants import FIFF
from .io.tree import dir... | matthew-tucker/mne-python | mne/source_space.py | Python | bsd-3-clause | 92,601 | [
"Mayavi"
] | 6cc6490b10d450bc32411390fc4347b1446635b0adc89717a71943866a7792ae |
import os
import sys
import time
import config
import numpy as np
from numpy import vectorize
from scipy import interpolate, integrate
from scipy import special
from scipy.interpolate import UnivariateSpline, InterpolatedUnivariateSpline
from scipy.ndimage.filters import gaussian_filter
import pylab as pl
from numba im... | vvinuv/HaloModel | halowlsz/halomodel_cl_tSZ_a_working.py | Python | gpl-3.0 | 8,691 | [
"TINKER"
] | 077ca2471d1b2af12575a8f663f7652ec701e1dc50ebd60fe3f6d754b57780ad |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Ior(AutotoolsPackage):
"""The IOR software is used for benchmarking parallel file systems
... | LLNL/spack | var/spack/repos/builtin/packages/ior/package.py | Python | lgpl-2.1 | 2,371 | [
"NetCDF"
] | 135d9bd2511426ed1c9ae3d536fc0a31e9447557422c6d0272ed44f4b5ccc93e |
# creates: diffusion-path.png
import os
from ase.io import read, write
if 1:
exec(compile(open('diffusion4.py').read(), 'diffusion4.py', 'exec'))
images = [read('mep%d.traj' % i) for i in range(5)]
a = images[0] + images[1] + images[2] + images[3] + images[4]
del a.constraints
a *= (2, 1, 1)
a.set_cell(images[0].g... | misdoro/python-ase | doc/tutorials/constraints/diffusion.py | Python | gpl-2.0 | 454 | [
"ASE"
] | 691aa23a3906ef548d111f67c287ddc2645da58d01a5e49f9817c71f77a5ca80 |
import emcee
import numpy as np
import math
import naxion
from quasi_observable_data import *
debugging = False
derived=False # quick hack for derived params
run_name='Example_Mtheory_run1'
startFile=False
startChainFile='Chains/Example_Mtheory_run1.npy'
if debugging:
import time
print 'starting'
#np.random.seed... | DoddyPhysics/AxionNet | Example_Mtheory_MCMC.py | Python | mit | 6,062 | [
"Gaussian"
] | 1e972782daf38c7ea4897b4e14c639f7aff786e0bb005cd224eaf0b690de9730 |
""" unit tests for Transformation Clients
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# pylint: disable=protected-access,missing-docstring,invalid-name
import six
import unittest
import json
import mock
from DIRAC.RequestManagementSystem.Client.Req... | yujikato/DIRAC | src/DIRAC/TransformationSystem/Client/test/Test_Client_TransformationSystem.py | Python | gpl-3.0 | 12,474 | [
"DIRAC"
] | 533730b466245279833e8bdd4371886895b6d3ebc2d6d39183d6a8233c6e682e |
import os
import sys
from Bio import Seq
from Bio import SeqIO
from Bio import SeqRecord
import pandas as pd
import numpy as np
import ms_module as ms
import re
############################
from Bio import Entrez
from Bio import SeqIO
from StringIO import StringIO
import time
from urllib2 import HTTPError # for Python... | sergpolly/GlycoMadness | stage1b_pull_proteins_NCBI.py | Python | mit | 5,272 | [
"Biopython"
] | 7004abaa4de9a05fb43d249b758d27070d7dd7d69b51f6ffa9bb5ea78277cae7 |
from __future__ import annotations
import math
from cctbx.crystal import symmetry
from libtbx.phil import parse
from dials.array_family import flex
from dials.util import tabulate
"""
Class to find a reasonable cutoff for integration based on work in LABELIT.
Bins the reflection table by resolution, then finds the ... | dials/dials | algorithms/integration/stills_significance_filter.py | Python | bsd-3-clause | 6,523 | [
"CRYSTAL"
] | 4f1ceabe4396af37c5d8ee7642ea7c8b78943643ad1b30dc3854538ac767d4c8 |
# Setup the broken Karaage test suite path
import sys
from os import path
from django.test import TestCase
from django.core.urlresolvers import reverse
from django.core.management import call_command
from tldap.test import slapd
from karaage.tests.initial_ldap_data import test_ldif
from fixtures import PersonFactory... | NeCTAR-RC/karaage-user | kguser/tests/test_username_change.py | Python | gpl-3.0 | 2,034 | [
"VisIt"
] | 57d070d873ff9a2475cf725607ccd33d7bc11d016c9ed23347ee13e05220e042 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/plugins/kgapplications/views/states.py | Python | gpl-3.0 | 19,613 | [
"Brian"
] | 36198812fd8a498d7da32ceb7d4d5b638982ac72be1ed8b9b82b012b2e5f8e06 |
#!/usr/bin/env python
import sys, os, copy, string, tempfile
class AtacRow:
"A general ATAC row object"
def __init__(self,line):
self.kind = line[0]
splitline = line[1:].split(">")
self.fixed = splitline[0].split()
if(len(splitline)>1):
self.defline = splitline[1]
... | peterhj/wgs-assembler | kmer/atac-driver/chainer/python/MatchRecord.py | Python | gpl-2.0 | 7,823 | [
"Brian"
] | 69aa2af5b825917a9f0b9d1d4fd4bb489be3b767f94c77b9c88ad39c512de1c2 |
""" StorageOccupancy records the Storage Elements occupancy over time
"""
from DIRAC.AccountingSystem.Client.Types.BaseAccountingType import BaseAccountingType
class StorageOccupancy(BaseAccountingType):
"""StorageOccupancy as extension of BaseAccountingType.
It is filled by the RSS Command FreeDiskSpace eve... | DIRACGrid/DIRAC | src/DIRAC/AccountingSystem/Client/Types/StorageOccupancy.py | Python | gpl-3.0 | 1,122 | [
"DIRAC"
] | 6d63402586a1159baca31bf81be274aa4907407341bf90d786142a851a98b9e4 |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006,2007,2012,2014,2015, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public v... | ghutchis/cclib | test/data/testvib.py | Python | lgpl-2.1 | 7,252 | [
"Dalton",
"Gaussian",
"ORCA",
"cclib"
] | 472f012274137b0013c9eb04c55b04ee130fdd2657f26ba02d808415c0a5b7c9 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/json_wrapper.py | Python | lgpl-3.0 | 7,560 | [
"Psi4"
] | f22af733a9013f024f6dcda68e260f963c03121fe5a90426a353f67048d8e2d6 |
from setuptools import setup
setup(name="pyurdme",
version="1.1.0",
packages=['pyurdme'],
#include_package_data = True,
package_data={'pyurdme':['data/*.c','data/three.js_templates/js/*','data/three.js_templates/*.html','urdme/AUTHORS','urdme/LICENCE','urdme/bin/*','urdme/build/*','urdme... | Molns/pyurdme | setup.py | Python | gpl-3.0 | 890 | [
"Brian"
] | 5b9d4c323716bfd3f237dab12a1a0771ab20a775f607c331f283a3423e244603 |
sdss_dir = '/auton/data/sdss/dr7/'
data_dir = ''
# code for features
feature_code={
'spectrum': 1,
'continuum': 2,
'spectrums1': 3,
'continuums1': 4,
'lines': 5,
'spectrum-color': 6,
'continuum-color': 7,
'spectrums1-color': 8,
'continuums1-color': 9,
}
similarity_code = {
... | excelly/xpy-ml | sdss/settings.py | Python | apache-2.0 | 9,314 | [
"Galaxy"
] | 91179a8a3ad6fb2aa6d04202ac1f5941230a84306d829bd91f7c69f4530c7a81 |
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