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"""
@brief test log(time=4s)
@author Xavier Dupre
"""
import sys
import os
import unittest
import warnings
from textwrap import dedent
from pyquickhelper.loghelper.flog import fLOG
from pyquickhelper.loghelper import run_cmd
from pyquickhelper.pycode import ExtTestCase, get_temp_folder
from pyquickhelper.helpg... | sdpython/pyquickhelper | _unittests/ut_helpgen/test_module_c.py | Python | mit | 7,882 | [
"VisIt"
] | 019d9622250483b1bfaf3d50c400a85860e5d4c58057c46316c8245e03b99b1a |
from hotbit import Hotbit
from ase import *
from hotbit.test.misc import default_param
from box.mix import Timer
from ase.lattice.cubic import FaceCenteredCubic
t=Timer()
#atoms = FaceCenteredCubic(directions=[[1,-1,0], [1,1,-2], [1,1,1]],
#size=(1,1,1), symbol='Au', pbc=(1,1,1))
... | pekkosk/hotbit | hotbit/test/size.py | Python | gpl-2.0 | 1,463 | [
"ASE"
] | a34284546793c91b59f0d0c23ac883636fda84da98c707554f01936be7c6f273 |
#
# Copyright (C) 2013,2014,2015,2016 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)... | lahnerml/espresso | samples/python/lj_liquid_structurefactor.py | Python | gpl-3.0 | 7,404 | [
"ESPResSo"
] | 97ba7477f35fba178ed6b3e1bb4d70efb11df08555baa5bcd4e74118c2b6f124 |
####################################################
## Wikipedia revision history crawling by article ##
## by Nicholas Bennett and Brian Keegan ##
## Copyright 2012 ##
####################################################
from wikitools import wiki, api
import random
import dateutil.parser
import codecs
impor... | tothebeat/wikipedia-revisions | usercontributions.py | Python | mit | 9,034 | [
"Brian"
] | eb5568f499ee0a29a8b0f35168d07ac708b4922c86bba0d1c8780490151f7c07 |
from scipy import stats
import seaborn as sns
import matplotlib.pyplot as plt
import pandas as pd
import requests
import json
ASE_DEFS = {
'11820001': 'ASE_NL01',
'11820002': 'ASE_NL02',
'11820003': 'ASE_NL03',
'11820004': 'ASE_NL04',
'11820005': 'ASE_NL05',
}
GAS_DEFS = {
'co': 'carbon_monoxi... | Geonovum/smartemission | etl/calibration/airsenseurplots.py | Python | gpl-3.0 | 5,001 | [
"ASE"
] | 4382855faff2e75c1ef28010e776b79f6b6bfb85b3ae76b20fd1bfbe43ad21ef |
#!/usr/bin/python
import numpy as np
import scipy as sp
from sys import *
######################## Define some vars #####################################
N_fd = 6145 # Num freq samples
dF = 1./3. # Frequency resolution of data
lowBin = int(10./dF) + 1 # Bin number corresponding to 10Hz - low
# frequency c... | bwengals/ccsnmultivar | ccsnmultivar/GWUtils.py | Python | mit | 19,596 | [
"Gaussian"
] | 9e87c1b091556552e1d2d0d39106310be9cb11c12f4cd4c862bb855e492a015e |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/coordinates/test_netcdf.py | Python | gpl-2.0 | 44,464 | [
"Amber",
"MDAnalysis",
"NetCDF"
] | c4d0fe0c21968f5c64a21411a224a5ceca44fa22cbb0133ed60d1fa95ea61525 |
import ambgmin_ as GMIN
import pele.potentials.gminpotential as gminpot
from pele.optimize import fire
import numpy as np
from copy import copy
from pele.potentials.potential import potential as BasePotential
from simtk.openmm.app import *
from simtk.openmm import *
from simtk.unit import *
import simtk.openmm.ap... | js850/pele | examples/amber/compare_with_ambgmin/OpenmmAmbPot.py | Python | gpl-3.0 | 5,215 | [
"Amber",
"OpenMM"
] | b0b50cee71436e645416f0cef2aaf994ea647196d2ebe1d82025947ee26fa4bc |
""" Test_RSS_Command_GOCDBStatusCommand
"""
__RCSID__ = '$Id$'
import unittest
import importlib
from datetime import datetime, timedelta
import mock
from DIRAC import gLogger, S_OK
from DIRAC.ResourceStatusSystem.Command.DowntimeCommand import DowntimeCommand
######################################################... | arrabito/DIRAC | ResourceStatusSystem/Command/test/Test_RSS_Command_GOCDBStatusCommand.py | Python | gpl-3.0 | 23,083 | [
"DIRAC"
] | fde82da8a6e77f0cafe04217e45a485b45e1700cbdb14750bb5cf8099b9cc9f5 |
# -*- encoding: utf-8 -*-
from __future__ import unicode_literals
import djclick as click
from django.conf import settings
from django.template.loader import render_to_string
from ...command_helpers import gather_event_date_from_prompt
from ...forms import EventForm
from ...models import Event
from pictures.models im... | patjouk/djangogirls | core/management/commands/new_event.py | Python | bsd-3-clause | 4,088 | [
"exciting"
] | 12c03e4d1f952c7b48f8569a94af5deb0838b7e721021dd25da9f6765677ac47 |
from rdkit import RDConfig
import os, sys, math
import unittest
import numpy as np
from rdkit import DataStructs
from rdkit import Chem
from rdkit.Geometry import rdGeometry as geom
from rdkit.Chem import rdMolTransforms as rdmt
def feq(v1, v2, tol=1.0e-4):
return abs(v1 - v2) < tol
def ptEq(pt, tpt, tol=0.0001):
... | rdkit/rdkit | Code/GraphMol/MolTransforms/Wrap/testMolTransforms.py | Python | bsd-3-clause | 11,290 | [
"RDKit"
] | 0a9efcb74a7c6315639bc452658ee45662aa1fa8b6f0b98a6a6e69759bb4b8f5 |
# Copyright 2015 CERN. This software is distributed under the
# terms of the GNU General Public Licence version 3 (GPL Version 3),
# copied verbatim in the file LICENCE.md.
# In applying this licence, CERN does not waive the privileges and immunities
# granted to it by virtue of its status as an Intergovernment... | kiliakis/BLonD | plots/plot.py | Python | gpl-3.0 | 11,026 | [
"Gaussian"
] | d14c7dc8f8b04c63945b2af2c8ed89694f7679d5f7ae103f20a0495d500ededc |
# Issue 47 on moose-core
import moose
print( '[INFO] Using moose from %s' % moose.__file__ )
# moose.loadModel('../data/acc94.g','/acc94','gsl')
moose.loadModel('../data/acc94.g','/acc94','gssa')
moose.reinit()
moose.run( 10 )
| subhacom/moose-core | tests/issues/issue_47.py | Python | gpl-3.0 | 227 | [
"MOOSE"
] | a240b8eb56a3f9e06c26845c266dcf8fc49129416ef561d2d009ad32c7d25edc |
# Copyright (c) 2018 PaddlePaddle Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except jin compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | PaddlePaddle/Paddle | python/paddle/fluid/dygraph/parallel.py | Python | apache-2.0 | 31,134 | [
"MOE"
] | 413c4d6d13870390504df24a58c6b8a5282e133f50a4fea8d481669ac697d42a |
from setuptools import setup
import os
description='SWC to VTK converter for visualize multi-compartment neurons and neural circuit simulations'
long_description = description
if os.path.exists('README.txt'):
long_description = open('README.txt').read()
setup(
name='swc2vtk',
version='1.1.1',
packages... | DaisukeMiyamoto/swc2vtk | setup.py | Python | apache-2.0 | 1,246 | [
"NEURON",
"ParaView",
"VTK"
] | a975c14122962a7ce191e9b4faef80979f108d64c7c45e4180af4ca6976dae46 |
import unittest, functools
from bashlex import parser, state, flags, ast, errors
parse = functools.partial(parser.parse, convertpos=True)
def reservedwordnode(word, s):
return ast.node(kind='reservedword', word=word, s=s)
def commandnode(s, *parts):
return ast.node(kind='command', s=s, parts=list(parts))
d... | blurrymoi/bashlex | tests/test-parser.py | Python | gpl-3.0 | 41,659 | [
"VisIt"
] | f1e87adbaacb883f62f67cf8ee0471d49b3853bed259e9faf438d0a9fd6d889a |
# -*- 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-analytics-admin | tests/unit/gapic/admin_v1alpha/test_analytics_admin_service.py | Python | apache-2.0 | 767,597 | [
"Octopus"
] | 5d848a9e64b26186478c1938bc4d3ef0269f1834ee1bd1f148c1c9fc288404d7 |
# ----------------------------------------------------------------------------
# Copyright (c) 2016-2017, QIIME 2 development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file LICENSE, distributed with this software.
# ------------------------------------------------... | gregcaporaso/q2cli | q2cli/info.py | Python | bsd-3-clause | 3,645 | [
"VisIt"
] | 5df0362e6693dc475a74b1c6c42bfbbf6ae94cfe8a386d63bd8894aca32d5e05 |
# -*- coding: utf-8 -*-
from collections import defaultdict
import os
import numpy as np
from pyfr.shapes import BaseShape
from pyfr.util import memoize, subclass_where
from pyfr.writers import BaseWriter
class VTKWriter(BaseWriter):
# Supported file types and extensions
name = 'vtk'
extn = ['.vtu', '.... | BrianVermeire/PyFR | pyfr/writers/vtk.py | Python | bsd-3-clause | 18,273 | [
"VTK"
] | c43b3a9689b01dc323d282bb93862164ba2875855f9931b756e60b58864e8938 |
# -*- coding: utf-8 -*-
"""
Data transformations
====================
The statistics of intermittent precipitation rates are particularly non-Gaussian
and display an asymmetric distribution bounded at zero.
Such properties restrict the usage of well-established statistical methods that
assume symmetric or Gaus... | pySTEPS/pysteps | examples/data_transformations.py | Python | bsd-3-clause | 7,504 | [
"Gaussian"
] | 923c707e1e3b23ad0c96f9b5abb5d6ed1a6943054dfe8ddea03a3c5a51e58e61 |
# coding: utf-8
import random
from django.contrib.auth.models import Permission
from django.contrib.auth.models import User
from django.core.management.base import BaseCommand
from kpi.models import Asset
from kpi.models import Collection
# random words
TAGS = ' '.join(['whale various alien cat witness before cliff ... | onaio/kpi | kpi/management/commands/tag_random_assets.py | Python | agpl-3.0 | 2,467 | [
"BLAST"
] | 0e096dd1aba7b66ad68edf2fa097c858f80b4a9c3af80db9371fe612dfb63fec |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | ctk3b/mdtraj | mdtraj/geometry/tests/test_hbonds.py | Python | lgpl-2.1 | 5,707 | [
"MDTraj",
"PyMOL"
] | 0166e7c9a6a8a73c40d0cc72a506e3d833e8a9f0150ff096a68f32c948fd3814 |
# ---
# jupyter:
# jupytext:
# formats: ipynb,.pct.py:percent
# text_representation:
# extension: .py
# format_name: percent
# format_version: '1.3'
# jupytext_version: 1.3.3
# kernelspec:
# display_name: Python 3
# language: python
# name: python3
# ---
# %% [markdown]
... | GPflow/GPflow | doc/source/notebooks/advanced/coregionalisation.pct.py | Python | apache-2.0 | 7,650 | [
"Gaussian"
] | abe322c257c08f730766d5f8864e8d7d741564492ffdb94c0b95df0117f593a1 |
"""
CBMPy: CBModelTools module
==========================
PySCeS Constraint Based Modelling (http://cbmpy.sourceforge.net)
Copyright (C) 2009-2022 Brett G. Olivier, VU University Amsterdam, Amsterdam, The Netherlands
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Gen... | SystemsBioinformatics/cbmpy | cbmpy/CBModelTools.py | Python | gpl-3.0 | 6,727 | [
"PySCeS"
] | a1bbf935a8ae41888115a2ca364a385a73cabcb35d3df087177f2c21f2bdbb44 |
import catmap
from catmap.model import ReactionModel
from catmap import ReactionModelWrapper
import numpy as np
import mpmath as mp
from ase.atoms import string2symbols
class SolverBase(ReactionModelWrapper):
def __init__(self,reaction_model=ReactionModel()):
"""Class for `solving' for equilibrium coverage... | ajmedford/catmap | catmap/solvers/solver_base.py | Python | gpl-3.0 | 10,530 | [
"ASE"
] | 4a39351bdea986efcfdd4d4b8eb8e8d20ff4acb8127c7b1cda2d043344521b5a |
import numpy as np
import ase
from ase.parallel import paropen
cfg_default_fields = np.array( [ 'positions', 'momenta', 'numbers', 'magmoms' ] )
def write_cfg(f, a):
"""Write atomic configuration to a CFG-file (native AtomEye format).
See: http://mt.seas.upenn.edu/Archive/Graphics/A/
"""
if isin... | slabanja/ase | ase/io/cfg.py | Python | gpl-2.0 | 6,713 | [
"ASE"
] | 049897f967b3ffc577b63cafc1ba1a2bae3ccba42c5f9a5130a6cd621dd5cd1a |
import numpy as np
import matplotlib.pyplot as plt
import sys
# Add the PyRsw tools to the path
# At the moment it is given explicitely.
# In the future, it could also be added to the
# pythonpath environment variable
sys.path.append('../src')
import Steppers as Step
import Fluxes as Flux
from PyRsw import Simulation... | PyRsw/PyRsw | examples/example_1D_geoadjust.py | Python | mit | 3,339 | [
"Gaussian"
] | e3cc8575321d64574c21ead90314da16c3d58bd29f2f55ea1bdccdba7d9fd900 |
import os
import zipfile
import shutil
import logging
import requests
import datetime
import pytz
from django.conf import settings
from django.core.exceptions import ObjectDoesNotExist
from django.core.files import File
from django.core.files.uploadedfile import UploadedFile
from django.core.exceptions import Validati... | hydroshare/hydroshare | hs_core/hydroshare/resource.py | Python | bsd-3-clause | 46,962 | [
"NetCDF"
] | cf2b6c9c59a212be13b98456d8348d42859857a283ff69e49db3f843de49082d |
# Optimize MGH suite with grid restrained Nelder-Mead optimizer.
from pyopus.optimizer.grnm import GRNelderMead
from pyopus.optimizer.base import Reporter
from pyopus.problems.mgh import *
from numpy import array, sqrt
from platform import system
if system()=='Windows':
# clock() is the most precise timer in Windows... | blorgon9000/pyopus | demo/optimizer/grnm.py | Python | gpl-3.0 | 4,200 | [
"Gaussian"
] | 4704932de0cc55930db8111173077ab9e65aaee4ca9d8310d6020d721ff0d05a |
from ..models import Visit, db
from sqlalchemy import func
import sys
PY3 = sys.version > '3'
if PY3:
from urllib.parse import urlparse
else:
from urlparse import urlparse
def count_visit(request, url=None):
"Inserts a record in visits model for current URL (excluding querystring)"
if not url:
... | kashifpk/pyckapps.visit_counter | lib/__init__.py | Python | apache-2.0 | 850 | [
"VisIt"
] | 806c3afda307fa1ccbe430672ebb776a1ce0379ec8de726f8c0bbfe30d798146 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/r-summarizedexperiment/package.py | Python | lgpl-2.1 | 2,476 | [
"Bioconductor"
] | d8a8ab974353d761f767544989c8e2fe24f0fc9d0936895b586390127a61656b |
# Copyright 2018 Open Source Robotics Foundation, 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... | ros2/launch | launch/launch/utilities/visit_all_entities_and_collect_futures_impl.py | Python | apache-2.0 | 1,837 | [
"VisIt"
] | e3fd8e053e370d284e6df7bceedf540a10412f881b37250d9cc4f1f942324428 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# chef2ldif documentation build configuration file, created by
# sphinx-quickstart on Tue Jul 9 22:26:36 2013.
#
# 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
# a... | brianchoate/chef2ldif | docs/conf.py | Python | bsd-3-clause | 8,465 | [
"Brian"
] | 189cdf1e76a0d53db36c4f7e78b5abbf91f0609670d86ef7dd9546094021a617 |
""" The Notification service provides a toolkit to contact people via email
(eventually SMS etc.) to trigger some actions.
The original motivation for this is due to some sites restricting the
sending of email but it is useful for e.g. crash reports to get to their
destination.
Another use-case is... | yujikato/DIRAC | src/DIRAC/FrameworkSystem/Service/NotificationHandler.py | Python | gpl-3.0 | 11,252 | [
"DIRAC"
] | 49a0a9170834942f5afb796cae11a3e9afcb5e8069b0cc3cf1005b7ac3fd4600 |
#!/usr/bin/env python3
#
# (C) 2016, Markus Wildi, wildi.markus@bluewin.ch
#
# 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, or (at your option)
# any later version.
#
... | zguangyu/rts2 | scripts/u_point/u_simulate.py | Python | gpl-2.0 | 20,995 | [
"Gaussian",
"VisIt"
] | acea506217ac8236023c3c0bc77cfbd45c8dbea35ff7e958ee09e591d9f2e7bf |
from numpy import array, arange, frombuffer, load, asarray, random, \
fromstring, expand_dims, unravel_index, prod
try:
buffer
except NameError:
buffer = memoryview
from ..utils import check_spark, check_options
spark = check_spark()
def fromrdd(rdd, nrecords=None, shape=None, index=None, labels=None, d... | j-friedrich/thunder | thunder/series/readers.py | Python | apache-2.0 | 14,279 | [
"Gaussian"
] | 0282505c55484d36e6ae3e85293e4bb7334962a3cf3d92062a647d6e80907576 |
import sys
import subprocess
def simread(refFile, inFastaFile, len_read, cov, out_dir, thread):
##[make reads]
cmdsim = ['dwgsim -1 %s -2 %s -C %s %s %ssim'%(len_read,len_read,cov,inFastaFile,out_dir)]
subprocess.call(cmdsim, shell=True)
##[make index]
cmdindex = ['bwa index %s'%(refFile)]
su... | bvalot/panISa | validate/util/simread.py | Python | gpl-3.0 | 1,137 | [
"BWA"
] | 5828e2ad60105e910c03aa885c5268a5603375fe38ec78893890536c2dc1bdb3 |
import numpy as np
import scipy
def lorentz(x, x0, gamma, intensity):
"""Compute complex lorentzian function.
The function is protected against negative unphysical arguments.
"""
x0 = abs(x0)
gamma = abs(gamma)
intensity = abs(intensity)
lor = intensity * np.divide(gamma * x0, pow(x0,2) - pow(x,2) - 1.0j * x... | francescorandi/optics | legacy/Oscillators.py | Python | gpl-3.0 | 2,151 | [
"Gaussian"
] | e8a112c8eb651146b035cd12a27d5552ec679a7f768275d6606efd10c1fcc4fb |
import sys
import numpy as nmp
def get_basin_info( cf_bm ):
from netCDF4 import Dataset
l_b_names = [] ; l_b_lgnms = []
l_b_names.append(u'GLO') ; l_b_lgnms.append(u'Global Ocean')
id_bm = Dataset(cf_bm)
list_var = id_bm.variables.keys()
for cv in list_var:
if cv[:5] == 'tmask':
... | plesager/barakuda | python/modules/barakuda_orca.py | Python | gpl-2.0 | 9,884 | [
"ORCA"
] | 00b4db72930aae959192f31f058453c34d580c43a6d1675582d8df7bbb3dadf8 |
"""A module that displays Parametric Surfaces, which are generated by
sets of equations describing the deformation of the real plane into
the surface.
"""
# Authors: KK Rai (kk.rai [at] iitb.ac.in)
# R. Ambareesha (ambareesha [at] iitb.ac.in)
# Prabhu Ramachandran (prabhu [at] aero.iitb.ac.in)
# Enth... | dmsurti/mayavi | mayavi/sources/parametric_surface.py | Python | bsd-3-clause | 4,516 | [
"Mayavi"
] | ec7d6b67134c66a73e356923f2819f7b0bde3c1d8bd52045f16c44f0bc28263a |
#
# script.py - non-interactive, script based anaconda interface
#
# Copyright (C) 2011
# Red Hat, Inc. All rights reserved.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 o... | mattias-ohlsson/anaconda | pyanaconda/script.py | Python | gpl-2.0 | 1,703 | [
"Brian"
] | 0a7b047e65f6c5a6c208dc9ff3e4cea1bb1e050a304ff80ca4188bbc2cd3eb3e |
#! /usr/bin/env python
import db
import math
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
import sys
from sets import Set
from rdkit import Chem
from rdkit.Chem import rdMolDescriptors
from rdkit.Chem import SDWriter
from sklearn.feature_selection import VarianceThreshold
data = db.getTarge... | PMitura/smiles-neural-network | baselines/rdkit_comp.py | Python | bsd-3-clause | 2,737 | [
"CDK",
"RDKit"
] | 6b2a1a0108708dda7be6e052d6facc75d1a951f87931c970bb5761037a710f41 |
"""Base class for mixture models."""
# Author: Wei Xue <xuewei4d@gmail.com>
# Modified by Thierry Guillemot <thierry.guillemot.work@gmail.com>
# License: BSD 3 clause
from __future__ import print_function
import warnings
from abc import ABCMeta, abstractmethod
from time import time
import numpy as np
from .. impor... | dsquareindia/scikit-learn | sklearn/mixture/base.py | Python | bsd-3-clause | 16,648 | [
"Gaussian"
] | 813be79db9815b9574fc2213d75bef010d71d4f042c5480160881a77c8294a99 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
#
# Copyright (C) 2017 Lenovo, Inc.
#
# 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 Licens... | tsdmgz/ansible | lib/ansible/modules/network/cnos/cnos_conditional_template.py | Python | gpl-3.0 | 8,735 | [
"VisIt"
] | 0f7fff0ef4790086566bf1004bb3cb47598a1363b32d2c8efb9722e7b287eb12 |
import numpy as np
from matplotlib import pyplot
from spm1d import rft1d
#(0) Set parameters:
np.random.seed(123456789)
nResponses = 8
nIterations = 2000
nNodes = 101
FWHM = 10.0
### derived parameters:
df = nResponses-1
sqrtN = np.sqrt(nResponses)
#(1) Generate Gaussian 1D fields, com... | 0todd0000/spm1d | spm1d/rft1d/examples/val_max_1_onesample_t_1d.py | Python | gpl-3.0 | 1,246 | [
"Gaussian"
] | 7bcfbad17422482c1b250d27bcc1eda619c8611c49f8549e17336f0e5a11a7f8 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""Wrappers for ABINIT main executables"""
from __future__ import unicode_literals, division, print_function
import os
import numpy as np
from monty.string import list_strings
from six.moves import map, cStrin... | setten/pymatgen | pymatgen/io/abinit/wrappers.py | Python | mit | 13,712 | [
"ABINIT",
"pymatgen"
] | 0bf28dd6ef158c5b7accb6459f422dd556e18a17a275c920e6d070780dc0053c |
"""The MIT License (MIT)
Copyright (c) 2016-2017 Marcus Ottosson
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify,... | oculusstorystudio/kraken | Python/kraken/ui/Qt.py | Python | bsd-3-clause | 26,917 | [
"VisIt"
] | 1a55e5b1801128062f546562b32720bb097c0ac24c602b151593bfaeb79c95e0 |
import numpy as np
from scipy.ndimage.filters import gaussian_filter
from .util import (DescriptorExtractor, _mask_border_keypoints,
_prepare_grayscale_input_2D)
from .brief_cy import _brief_loop
from .._shared.utils import assert_nD
class BRIEF(DescriptorExtractor):
"""BRIEF binary descript... | newville/scikit-image | skimage/feature/brief.py | Python | bsd-3-clause | 7,094 | [
"Gaussian"
] | 997304f790e4aaa49b0836f58d5b15080f3fb4c8ecbc7625ee8d1f6633fb09d6 |
# Propagate labels upwards to label the empty space
# May 2016 - Martijn Koopman
# ToDo: Clean code; Pass variable dims to function GetArrValue() and SetArrValue() as arguments.
# Read input
idi = self.GetInput()
dims = idi.GetDimensions()
numTuples = dims[0]*dims[1]*dims[2]
arr = idi.GetPointData().GetSca... | martijnkoopman/thesis | 2_5_propagate_labels_up.py | Python | gpl-3.0 | 1,243 | [
"VTK"
] | 474f132f567c6c299a4fcb67211144b5372100e9586ac4b936a6d253fafb60bf |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
from PyQt5 i... | nuclear-wizard/moose | python/peacock/Input/plugins/MeshCameraPlugin.py | Python | lgpl-2.1 | 937 | [
"MOOSE"
] | ada47711bfc7df84b26cbb04de5aab1a7527fa2d74d049e95d5c480dbdfebdf3 |
# Copyright 2017 The TensorFlow Authors All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | alexgorban/models | research/pcl_rl/env_spec.py | Python | apache-2.0 | 6,012 | [
"Gaussian"
] | b1aea860137173210b637090a9198d6c97cf96c627ed2c3572ad243900cacc1b |
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_chr13.py | Python | mit | 32,998 | [
"MCell"
] | d6b48277b018232a3ef139499842a540e87e7e28f61ed12ab9682395ffa8dbcd |
"""
This is our testing framework.
Goals:
* it should be compatible with py.test and operate very similarly
(or identically)
* doesn't require any external dependencies
* preferably all the functionality should be in this file only
* no magic, just import the test file and execute the test functions, that's it
* po... | wolfram74/numerical_methods_iserles_notes | venv/lib/python2.7/site-packages/sympy/utilities/runtests.py | Python | mit | 80,104 | [
"VisIt"
] | 6abf7f9840fe11790db41d916aa882d3de70eb67c2bda673bfe4d19b16078348 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either v... | Forage/Gramps | gramps/gen/plug/menu/_destination.py | Python | gpl-2.0 | 3,134 | [
"Brian"
] | a4322697f1bc7f383cd7750f8ab669a3b1ef4993cac8a5b1fd39ef2aae90fa7a |
import HTMLParser
import json
import random
import re
import urllib2
import urlparse
import requests
def clean_title(title):
if title == None: return
title = str(title)
title = re.sub('&#(\d);', '', title)
title = re.sub('(&#[0-9]+)([^;^0-9]+)', '\\1;\\2', title)
title = title.replace('"', '\... | mrquim/mrquimrepo | script.module.nanscrapers/lib/nanscrapers/common.py | Python | gpl-2.0 | 14,270 | [
"MOE"
] | 1437918d85968cdf41f124e8eeaf7aaabea72fce397cdac60f0a3e8005b931f2 |
# 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... | aldian/tensorflow | tensorflow/python/keras/activations.py | Python | apache-2.0 | 17,918 | [
"Gaussian"
] | cafed03981812fb0548b20de7a8dff64fa88fd8a72232cebc3d08bbcc9aa8678 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2006-2007 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 Fou... | andrebellafronte/stoq | stoqlib/domain/test/test_payment.py | Python | gpl-2.0 | 17,211 | [
"VisIt"
] | f66798e2086392a65418e02e1084af37761552aa6f6e09735983bd3bff08ee1f |
#!/usr/bin/env python
#
# IP Lookup script.
# Expects a tab delimited list of: IP, PAGES, HITS, BANDWIDTH, LAST VISIT
# The first column (IP) is required. Others are optional.
#
# This script uses a local settings module that the user must provide that
# contains an address to be used to look up IPs. This script is mea... | kd0kfo/stats_analyzer | scripts/lookup.py | Python | gpl-3.0 | 2,677 | [
"VisIt"
] | c90f0dee299ec0920fd445e0998fb58ef279de07b7a40f6cbfe67697da4160a6 |
import vtk
import math
import numpy as np
atp_min = 0.2
atp_max = 0.7
if __name__ == "__main__":
# Read ECs.
ecReader = vtk.vtkXMLPolyDataReader()
ecReader.SetFileName('quadMeshFullECc256.vtp')
ecReader.Update()
# Rememeber the cells.
polydata = ecReader.GetOutput()
# Create new ATP map... | BlueFern/DBiharMesher | meshes/c256f/Generate256ATPMeshVar.py | Python | gpl-2.0 | 2,088 | [
"VTK"
] | 15ebf21b5b80414037db133912a41dd79975bd005610b36d4118d5510aa025fe |
# accounts low-dimensional cases in 3D
# (NB the PW-based codes are forced to put vacuum in a "non-periodical" direction)
# extends ASE object(s)
# Author: Evgeny Blokhin
# TODO: account all "pseudo-periodic" cases for 1d and 0d
import math
from numpy import cross
from numpy.linalg import det
from numpy.linalg impor... | ansobolev/tilde | tilde/classifiers/dimensions.py | Python | mit | 2,246 | [
"ASE"
] | bf9ea389a000cc5a06a03763060707bd2a7db944448234ef95c5abbf1769d3cf |
#!/usr/bin/env python
import sys
import os
import vtk
sys.path.append(os.path.abspath('../../python'))
import lsutils
camera = vtk.vtkCamera()
camera.SetViewUp(0.0000, 1.0000, 0.0000)
camera.SetPosition(0.5000, 0.5000, 1.8660)
camera.SetFocalPoint(0.5000, 0.5000, 0.0000)
lsutils.build_frames(camera=camera)
| yipenggao/moose | modules/level_set/examples/vortex/viewer.py | Python | lgpl-2.1 | 311 | [
"VTK"
] | 1aadb7fd679137aca0dcf2e9ce25234c2e718b8cdbf1ba0f6aaef00f23939869 |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Definitions of derived coordinates.
"""
from abc import ABCMeta, abstractmethod
import warnings
import dask.array as da
... | pp-mo/iris | lib/iris/aux_factory.py | Python | lgpl-3.0 | 66,459 | [
"NetCDF"
] | af96d4c5771d80ccb2d7cbcff8204964281ccf76ed2d1e3b41608ef2a4ce1d10 |
"""
Copyright (c) 2009 John Markus Bjoerndalen <jmb@cs.uit.no>,
Brian Vinter <vinter@nbi.dk>, Rune M. Friborg <rune.m.friborg@gmail.com>.
See LICENSE.txt for licensing details (MIT License).
"""
import sys
sys.path.insert(0,"..")
if len(sys.argv) > 1:
mod = sys.argv[1]
else:
mod = ''
if (mod == 'parall... | runefriborg/pycsp | examples/pycsp_import.py | Python | mit | 552 | [
"Brian"
] | 2220e73bcae53bdbf246faae66c5631de3b8fa28e8a2e3b9ff05ecc54cd53a89 |
# $HeadURL$
__RCSID__ = "$Id$"
""" This backend just print the log messages through the standar output
"""
from DIRAC.FrameworkSystem.private.logging.backends.BaseBackend import BaseBackend
import sys
class PrintBackend( BaseBackend ):
COLOR_MAP = {
'black' : 0,
'red' : 1,
'green' : 2,
... | Andrew-McNab-UK/DIRAC | FrameworkSystem/private/logging/backends/PrintBackend.py | Python | gpl-3.0 | 1,425 | [
"DIRAC"
] | a04cc117c0e57a23155ffc2de247ad61d94bb0c581a5ebf7146715e34139db90 |
"""
Quadratic Discriminant Analysis
"""
# Author: Matthieu Perrot <matthieu.perrot@gmail.com>
#
# License: BSD 3 clause
import warnings
import numpy as np
from .base import BaseEstimator, ClassifierMixin
from .externals.six.moves import xrange
from .utils import check_array, check_X_y
from .utils.validation import ... | WangWenjun559/Weiss | summary/sumy/sklearn/qda.py | Python | apache-2.0 | 7,682 | [
"Gaussian"
] | eab0026b55f58914d88faf46266ca8eb9295a793bc30343cf5705692a23d23bf |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
# CREATED:2015-02-14 19:13:49 by Brian McFee <brian.mcfee@nyu.edu>
'''Unit tests for time and frequency conversion'''
import os
try:
os.environ.pop('LIBROSA_CACHE_DIR')
except KeyError:
pass
import warnings
import librosa
import numpy as np
import pytest
def te... | carlthome/librosa | tests/test_time_frequency.py | Python | isc | 14,857 | [
"Brian"
] | ea815b6cd2045b18db2efbbfc46793749bc7cd7d71201ef78d872b47ed86d0d2 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# jobaction - Change state of a waiting or running job
# Copyright (C) 2003-2010 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 Genera... | heromod/migrid | mig/cgi-bin/jobaction.py | Python | gpl-2.0 | 1,091 | [
"Brian"
] | 28138f2694388e870b16bf67eddc6acfac18bef4049af4c66cfd98ac610c2863 |
import numpy as np
import pandas as pd
# VTK imports:
import vtk
from vtk.numpy_interface import dataset_adapter as dsa
from base import TestBase
from PVGeo import interface
# Functionality to test:
from PVGeo._helpers import xml
RTOL = 0.000001
class TestXML(TestBase):
"""
Test the XML Helpers to make su... | banesullivan/ParaViewGeophysics | tests/helpers_test.py | Python | bsd-3-clause | 2,910 | [
"VTK"
] | 7868528fd26eb17216210f8a179ddbafd1ea22ff8221318c71067b1a7dddfd22 |
"""This module defines an indenter class that handles indentation
levels for automatic code generation. It also defines other
miscellaneous classes useful for the tvtk code generation.
"""
# Author: Prabhu Ramachandran
# Copyright (c) 2004, Enthought, Inc.
# License: BSD Style.
import re
# Local imports (there is ... | liulion/mayavi | tvtk/indenter.py | Python | bsd-3-clause | 8,570 | [
"VTK"
] | 89fc4c00eada51d4c49dbf2f7f22267da45b20ffc9b4a638584a2d8682a6992a |
# 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)
#
# This is a based largely on the Homebrew science formula:
# https://github.com/Homebrew/homebrew-science/blob/master/bl... | rspavel/spack | var/spack/repos/builtin/packages/blast-plus/package.py | Python | lgpl-2.1 | 7,172 | [
"BLAST"
] | d904c8331fe8be41b39b6bc0c23ed09c2bf2f7b2cd7170c5da98b8c3277385b6 |
""" DowntimeCommand module will look into GOC DB to find announced downtimes for RSS-managed sites and resources.
If found, downtimes are added to the internal RSS cache using ResourceManagementClient.
GOCDB downtimes that are modified or deleted are also synced.
"""
import re
from urllib.error import URLError... | DIRACGrid/DIRAC | src/DIRAC/ResourceStatusSystem/Command/DowntimeCommand.py | Python | gpl-3.0 | 15,366 | [
"DIRAC"
] | 58adad47419509483d2ad9b047a5aa0810294964b56a1d2ef3a069eb1f972601 |
import math
import random
import time
print('You have ten wrong chances in hangman.')
level = input('What level do you want from 1 to 12 or random?\n')
while level != '1' and level != '2' and level != '3' and level != '4' and level != '5' and level != '6' and level != '7' and level != '8' and level != '9' and level !=... | yrafalin/7thGrade | Hangman.py | Python | bsd-3-clause | 1,962 | [
"Galaxy"
] | 2afbc10605ffa28140f21cc4a56d4e6901cdcf06ed7c5642c3ebf9c52c22f5fe |
# -*- coding: utf-8 -*-
# Generated by Django 1.9.4 on 2016-03-18 14:30
from __future__ import unicode_literals
from django.db import migrations, models
import django.db.models.deletion
class Migration(migrations.Migration):
dependencies = [
('constellations', '0002_constellation_brightest_star'),
... | craigderington/SagittariusA | milkyway/galaxies/migrations/0002_galaxy_constellation.py | Python | gpl-3.0 | 632 | [
"Galaxy"
] | 8996f5ec855c4ed8dea354fa1625894ebca8924217da5eb769cc1ee5974bd236 |
# Make a CSV file of the beam sizes for all the Radio Galaxy Zoo sources
# Get list of the subjects from MongoDB
import rgz
subjects,classifications = rgz.load_rgz_data()
first_ids = []
for s in subjects.find():
first_ids.append(s['metadata']['source'])
atlas_ids = [x for x in first_ids if x[0] == 'C']
# Klug... | willettk/rgz-analysis | python/make_beamsize_list.py | Python | mit | 1,744 | [
"Galaxy"
] | ef3f2b5bcb2dc0424481b9af251738e56361d997b8ae539a9c50ef369b344dba |
from ase.data.molecules import molecule
from gpaw import GPAW
from gpaw import dscf
from gpaw.test import equal
# Ground state calculation
calc = GPAW(mode='lcao',
basis='dzp',
nbands=8,
h=0.2,
xc='PBE',
spinpol=True,
convergence={'energy': 100,
... | qsnake/gpaw | gpaw/test/dscf_lcao.py | Python | gpl-3.0 | 1,101 | [
"ASE",
"GPAW"
] | 54a2f66828d6ad8beb2b23230211c5239e034b02fdd9e9e50fa2b9cf630a7809 |
#!/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': ... | Jorge-Rodriguez/ansible | lib/ansible/modules/packaging/os/package_facts.py | Python | gpl-3.0 | 7,183 | [
"Brian"
] | 95356db062ad0fbd23f75e9767b7b4b59829b712414284100b83cf5e1660c566 |
#!/usr/bin/env python
#from sumatra.projects import load_project
#from sumatra.parameters import build_parameters
#from sumatra.decorators import capture
from ruffus import *
import sys
import os
import time
import datetime
import drmaa
from omics_pipe.utils import *
from omics_pipe.parameters.default_pa... | adammaikai/OmicsPipe2.0 | omics_pipe/WES_GATK.py | Python | mit | 3,381 | [
"BWA"
] | bbfbfc813aa940cb244213534c652297753a0cd2adf8f1f1f6918cc84034e5cd |
from __future__ import print_function
from os.path import dirname,basename,abspath,exists
import os
from functools import partial
import argparse
import shlex
import subprocess
import sys
from bio_bits.compat import OrderedDict, open
import sh
# Users cannot have these in the other args passed
STATIC_BLAST_ARGS = [
... | VDBWRAIR/bio_bits | bio_bits/parallel_blast.py | Python | gpl-2.0 | 8,787 | [
"BLAST"
] | c02de66feaffdafb3a41a62a273363ed446f7b81be1d5d9593dd57f64f45458d |
# -*- coding: ISO-8859-1 -*-
#############################################
## (C)opyright by Dirk Holtwick, 2002-2007 ##
## All rights reserved ##
#############################################
__reversion__ = "$Revision: 20 $"
__author__ = "$Author: holtwick $"
__date__ = "$Date: 20... | pombreda/xhtml2pdf | sx/pisa3/pisa_parser.py | Python | gpl-2.0 | 22,193 | [
"VisIt"
] | cb9ff08ba6fff0f9a98c0d6b39538fcdacf83203903912a917e590064a3ed402 |
# The Hazard Library
# Copyright (C) 2012 GEM Foundation
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# Th... | ROB-Seismology/oq-hazardlib | openquake/hazardlib/gsim/chiou_youngs_2008.py | Python | agpl-3.0 | 14,566 | [
"Brian"
] | 103dc3cdf4271f38a8596255b88391197c0258990f3a8288111b25133319d141 |
from __future__ import division
from collections import Counter
from functools import partial
from linear_algebra import dot
import math, random
import matplotlib
import matplotlib.pyplot as plt
def step_function(x):
return 1 if x >= 0 else 0
def perceptron_output(weights, bias, x):
"""returns 1 if the percep... | jljones/data-science-from-scratch | code/neural_networks.py | Python | unlicense | 6,623 | [
"NEURON"
] | 95774c358b1d0691041592fd07805d7c05f4b626deb50efb7320cc921725dd09 |
# Copyright 2000-2009 by Iddo Friedberg. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
# Iddo Friedberg idoerg@cc.huji.ac.il
"""Substitution matrices, log odds matrices, and... | bryback/quickseq | genescript/Bio/SubsMat/__init__.py | Python | mit | 22,839 | [
"Biopython"
] | 97efada8a5f9e67bc6707616bbd6de211f22c7189837041fefbc3fe42c31c0e4 |
"""
:mod: RSSCache
Extension of DictCache to be used within RSS
"""
__RCSID__ = '$Id$'
import datetime
import threading
import time
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities.DictCache import DictCache
class RSSCache(object):
'''
Cache with purgeThread integrated
'''
def __init__(self, li... | fstagni/DIRAC | ResourceStatusSystem/Utilities/RSSCache.py | Python | gpl-3.0 | 5,759 | [
"DIRAC"
] | 0881e490277c5d3b870d67f7e21b7157875e962de7eabdb8cdc3726cfbd23a8d |
"""
Tests for ob_utils.
"""
import numpy as np
import unittest
from rdkit import Chem
from rdkit_utils import conformers
from vs_utils.utils import ob_utils
class TestIonizer(unittest.TestCase):
"""
Test Ionizer.
"""
def setUp(self):
"""
Set up tests.
"""
smiles = 'CC... | rbharath/pande-gas | vs_utils/utils/tests/test_ob_utils.py | Python | bsd-3-clause | 4,073 | [
"RDKit"
] | 0a5fe611766e9dddece518f5060878d9f229cf3fffbf3efd16c3131ede52f72d |
# Author: Prabhu Ramachandran, Gael Varoquaux
# Copyright (c) 2004-2014, Enthought, Inc.
# License: BSD Style.
""" A tool for easy and interactive visualization of data.
Part of the Mayavi project of the Enthought Tool Suite.
"""
__version__ = '4.4.4.dev0'
__requires__ = [
'apptools',
'traits',
'trait... | dmsurti/mayavi | mayavi/__init__.py | Python | bsd-3-clause | 772 | [
"Mayavi"
] | 608b6bb07918ef68d41dc5761cb774e658c8d3ad32af83639455820fdbcb1eea |
# This file is part of CO𝘕CEPT, the cosmological 𝘕-body code in Python.
# Copyright © 2015–2022 Jeppe Mosgaard Dakin.
#
# CO𝘕CEPT 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 Lice... | jmd-dk/concept | src/interactions.py | Python | gpl-3.0 | 142,305 | [
"Gaussian"
] | 835f91fceaaeb933acc112f5c77cc329d73cb690f4b8769493c7f4889319d1bf |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. ... | Clyde-fare/cclib | src/cclib/bridge/__init__.py | Python | lgpl-2.1 | 850 | [
"cclib"
] | d4591b5c3992abcbe4e26a2e65fecd508938f314cf2fed03aafc2d73c5c29b24 |
from go_to_adjacent_systems import *
from go_somewhere_significant import *
import vsrandom
import launch
import faction_ships
import VS
import Briefing
import universe
import unit
import Director
import quest
class defend (Director.Mission):
def __init__ (self,factionname,numsystemsaway, enemyquantity, distance_fr... | vegastrike/Assets-Production | modules/missions/defend.py | Python | gpl-2.0 | 8,711 | [
"VisIt"
] | 2b451cc13cb2f2d6e7bcce1d007dc02420b1e52c01e2959473874801b8e75b1a |
commonly_used_passwords = [
'govuknotify',
'GOVUKnotify',
'GOV.UK Notify',
'GOV.UK notify',
'gov.uk notify'
] + [
'11111111',
'12345678',
'123456789',
'access14',
'alejandra',
'alejandro',
'baseball',
'bigdaddy',
'butthead',
'cocacola',
'computer',
'co... | alphagov/notifications-admin | app/main/_commonly_used_passwords.py | Python | mit | 116,613 | [
"COLUMBUS",
"ESPResSo"
] | ecaf14bf91e132c4f5f0f69f32a32e29af9601819f899a2ffc02ddfef80db83f |
""" Module that contains simple client access to Matcher service
"""
__RCSID__ = "$Id$"
from DIRAC.Core.Base.Client import Client
class MatcherClient(Client):
""" Exposes the functionality available in the WorkloadManagement/MatcherHandler
This inherits the DIRAC base Client for direct execution of server... | andresailer/DIRAC | WorkloadManagementSystem/Client/MatcherClient.py | Python | gpl-3.0 | 582 | [
"DIRAC"
] | dc66bdcfba5497d8f0582fa8890e524cfa708c8cece882dcf186a4eb4c45508b |
# TODO: to be transformed into a real test
########################################################################
# File: ReplicateAndRegisterTests.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/05/13 18:38:55
########################################################################
""" :mod: FullChainTest
... | chaen/DIRAC | tests/Integration/RequestManagementSystem/FIXME_IntegrationFCT.py | Python | gpl-3.0 | 6,241 | [
"DIRAC"
] | db74409ddd550ea901aa3cececb7229f51fbebf3b296fe2470dd7456d9becc44 |
# coding: utf-8
"""
A Flow is a container for Works, and works consist of tasks.
Flows are the final objects that can be dumped directly to a pickle file on disk
Flows are executed using abirun (abipy).
"""
from __future__ import unicode_literals, division, print_function
import os
import sys
import time
import collec... | rousseab/pymatgen | pymatgen/io/abinitio/flows.py | Python | mit | 92,896 | [
"ABINIT",
"pymatgen"
] | ac3ea3b6de80f7fb0fd04e813cd821bdf69d6214247bf456786673ef4b8f9c21 |
# coding=utf-8
# GENERAL PACKAGES ############################################################
import sys
import math
import numpy as np
import logging
from os.path import splitext
from math import log
from hyperspectral import HyperspectralCube as Cube
from matplotlib import pyplot as plot
logging.basicConfig(level=... | irap-omp/deconv3d | lib/run.py | Python | mit | 42,027 | [
"Galaxy",
"Gaussian"
] | 32c87a674bc93c9887db0fa0a78710d698fba5da8c8725aec4e933cbde43976d |
#!/usr/bin/python
from numpy import pi, array
from numpy.random import random
from numpy.linalg import norm
import time
import localizer
import robot, particles, map
from sensors import Ultrasonic
from pose import Pose
import std_sensors
import std_noise
import matplotlib.pyplot as plt
import argparse
import signal... | IEEERobotics/high-level | qwe/localizer/pftest.py | Python | bsd-2-clause | 4,235 | [
"Gaussian"
] | 48c678eeed37aba35490eda37334e8dbdd28ec1761d47808cb640a7d35ea94d7 |
"""
mathFunctions (:mod:`skrf.mathFunctions`)
=============================================
Provides commonly used mathematical functions.
Mathematical Constants
----------------------
Some convenient constants are defined in the :mod:`skrf.constants` module.
Complex Component Conversion
---------------------------... | scikit-rf/scikit-rf | skrf/mathFunctions.py | Python | bsd-3-clause | 28,547 | [
"DIRAC"
] | 0e199837dc0a4b4ff5139fdcb0439355189e2a447911a7c264be9d3a3f197332 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# 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 Public License as published by
# the Fr... | beernarrd/gramps | gramps/gen/plug/__init__.py | Python | gpl-2.0 | 2,745 | [
"Brian"
] | 038dadcae0d53c4502de8cecb0fe9ce87cf747d3a92c7358acecae8633e7f068 |
#!/usr/bin/env python
"""Provide a parser for SwissProt EBI format files.
"""
import sys
from string import maketrans, strip, rstrip
from pprint import pprint, pformat
from cogent.parse.record_finder import DelimitedRecordFinder,\
LabeledRecordFinder, is_empty, TailedRecordFinder
from cogent.parse.record import Re... | sauloal/cnidaria | scripts/venv/lib/python2.7/site-packages/cogent/parse/ebi.py | Python | mit | 58,303 | [
"Dalton"
] | 3850b2700f455a91a726522329fab9d7c02dd23ecef6fbf1d9c923c14cc7bd66 |
"""
Created on 12/8/2014
@author: victor
"""
import os
import prody
import sys
import json
from datetime import datetime
import hivprotmut.tools as tools
from hivprotmut.sequences.fastaFile import FastaFile
from hivprotmut.structures.pdbcuration import curate_struct, choose_main_chains
from hivprotmut.external.blast.b... | victor-gil-sepulveda/PhD-HIVProteaseMutation | hivprotmut/curateDB.py | Python | mit | 4,797 | [
"BLAST"
] | f4e6b33239a23d757c646c84394efb612222bf41fbda2a5a170d7825a8de357e |
# -*- 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 Lesser General Public License as published by
## the Free Software F... | Vauxoo/stoqdrivers | stoqdrivers/printers/bematech/MP2100TH.py | Python | lgpl-2.1 | 2,542 | [
"VisIt"
] | c8c5303426bc74058f2ecdfcb45565a4f8bcc1517c14812a6d6ecd79595dd975 |
#A* -------------------------------------------------------------------
#B* This file contains source code for the PyMOL computer program
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
#D* -------------------------------------------------------------------
#E* It is unlawful to modify or remove ... | gratefulfrog/lib | python/chempy/bond_mmff.py | Python | gpl-2.0 | 4,213 | [
"PyMOL"
] | 53ac9232d3151499e7753c9378852a9da01af6259eb8c2607caf384869c53fe8 |
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