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'''Points (dots, vectors) for PyMOLProbity plugin.'''
from __future__ import absolute_import
import copy
import logging
import re
from chempy import cpv
#from pymol import cmd
from pymol import cgo
from . import colors
# from settings import mpgetq
from . import utils
logger = logging.getLogger(__name__)
######... | jaredsampson/pymolprobity | pymolprobity/points.py | Python | mit | 24,345 | [
"ChemPy",
"PyMOL"
] | bd7afc8fe9dd59a94a5157b8cbcd47b81c3ae8f28fa0b8a268034ab50a8d2ac5 |
#!/usr/bin/python
########################################################################
# 31 Oct 2014
# Patrick Lombard, Centre for Stem Stem Research
# Core Bioinformatics Group
# University of Cambridge
# All right reserved.
########################################################################
import subproce... | pdl30/pynoncode | pynoncode/plot.py | Python | gpl-2.0 | 16,666 | [
"HTSeq"
] | dfd8e57793e72758161e9b281d5844e947cb64d48848d077cbb2fd283ca267e8 |
import random
import threading
import time
import unittest
from traits.api import Enum, HasStrictTraits
from traits.util.async_trait_wait import wait_for_condition
class TrafficLights(HasStrictTraits):
colour = Enum('Green', 'Amber', 'Red', 'RedAndAmber')
_next_colour = {
'Green': 'Amber',
... | burnpanck/traits | traits/util/tests/test_async_trait_wait.py | Python | bsd-3-clause | 2,297 | [
"Amber"
] | e7492efd21313d9d9cc8e2a966984afbbe6db1207a545cb76b5669c31ec3fe57 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Memsurfer(PythonPackage):
"""MemSurfer is a tool to compute and analyze membrane surfaces... | iulian787/spack | var/spack/repos/builtin/packages/memsurfer/package.py | Python | lgpl-2.1 | 1,848 | [
"NetCDF",
"VTK"
] | 509dd57371d7e388bbedf586e6879853ca3088e2f3bee9d2078db1933792389c |
__all__ = [
'BadRequestException',
'BadStateException',
'CsrfException',
'DropboxOAuth2Flow',
'DropboxOAuth2FlowNoRedirect',
'NotApprovedException',
'OAuth2FlowNoRedirectResult',
'OAuth2FlowResult',
'ProviderException',
]
import base64
import os
import six
import urllib
from .sessi... | mrquim/mrquimrepo | script.xbmcbackup/resources/lib/dropbox/oauth.py | Python | gpl-2.0 | 18,272 | [
"VisIt"
] | 36d380bd9046a0cd7483c2165be730eb9150fa88d193d124d6845785ae9559ae |
#
# AtHomePowerlineServer - networked server for CM11/CM11A/XTB-232 X10 controllers
# Copyright (C) 2014 Dave Hocker
#
# 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, version 3 of the Lic... | dhocker/athomepowerlineserver | drivers/X10ControllerAdapter.py | Python | gpl-3.0 | 4,887 | [
"xTB"
] | d883360244c933f68027b4d48ada23be49e6bb0ca7009032284d4e1d2d1010c0 |
# Copyright (c) 2012 OpenStack Foundation.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | yanheven/neutron | neutron/tests/unit/test_policy.py | Python | apache-2.0 | 26,323 | [
"BLAST"
] | 388d7e82d9d3aed253196a52b4c61b7802ba60f0c4c0176df86bb20f5fb7c796 |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | fweik/espresso | testsuite/scripts/tutorials/test_ferrofluid_1.py | Python | gpl-3.0 | 1,332 | [
"ESPResSo"
] | 87220fafa47da492171107851052bb5450eb7e15e90742ed69f8456b0646d8dc |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Created on July 31 09:51:20 2014
@author: Mathieu Garon
@email: mathieugaron91@gmail.com
"""
import roslib; roslib.load_manifest('picam_tracker_py')
import rospy
from sensor_msgs.msg import Image
import std_srvs.srv
import cv2
import picamera
import wiringpi2 as gpio... | iamblusky/Led_Tracking | src/picam_tracker_py/scripts/picam_timer.py | Python | bsd-2-clause | 6,348 | [
"Gaussian"
] | 7416afeae7bedd17c9e5aaea54c6981f63156b56fccc7607b0252207384bb3d4 |
from jobman import DD, expand, flatten
import pynet.layer as layer
from pynet.model import *
from pynet.layer import *
from pynet.datasets.mnist import Mnist, Mnist_Blocks
import pynet.datasets.spec as spec
import pynet.datasets.mnist as mnist
import pynet.datasets.transfactor as tf
import pynet.datasets.mapping as ... | hycis/Pynet | hps/models/RecSys.py | Python | apache-2.0 | 3,023 | [
"Gaussian"
] | 629f7d291c14e4b8928e68644ba6f720e77d69d12b521fbf1ecc700a024e2472 |
import os
import warnings
import numpy as np
from .. import DataArray
from ..core import indexing
from ..core.utils import is_scalar
from .common import BackendArray
from .file_manager import CachingFileManager
from .locks import SerializableLock
# TODO: should this be GDAL_LOCK instead?
RASTERIO_LOCK = Serializable... | jhamman/xarray | xarray/backends/rasterio_.py | Python | apache-2.0 | 12,938 | [
"NetCDF"
] | 817bc51d27b007fc96a7793826c2a3adba364381a717c51a8a60c0cf544cbc15 |
# -*- coding: UTF-8 -*-
# Copyright (C) 2016 Sylvain Taverne <taverne.sylvain@gmail.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) ... | nicolasderam/itools | itools/pkg/build_gulp.py | Python | gpl-3.0 | 2,833 | [
"GULP"
] | aeca73d821aa0ca78307db38d075d33b77705a9d9e385987a562b9bdd3d7b308 |
#!/usr/bin/env python
"""Tests for Genetic Algorithm Repair code.
This tests classes which are designed for repairing organisms after
mutation and crossover.
"""
# standard library
import unittest
# biopython
from Bio.Alphabet import Alphabet
from Bio.Seq import MutableSeq
# local stuff
from Bio.NeuralNetwork.Gene.S... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_GARepair.py | Python | gpl-2.0 | 2,135 | [
"Biopython"
] | 50658461bf764ad2a86f2e7f574e8d5b6914d4a03790b56b7dadd58bffdf961c |
import sys
import time as tm
import numpy as np
import ConfigParser
def getlist(option, sep=',', chars=None):
"""Return a list from a ConfigParser option. By default,
split on a comma and strip whitespaces."""
return [float(chunk.strip(chars)) for chunk in option.split(sep)]
class dnf:
def __init... | gdetor/neuralfieldDBSmodel | src/protocolEfficiency.py | Python | bsd-3-clause | 9,182 | [
"Gaussian",
"NEURON"
] | ca325e937129ce7a0caee81e76e56f0eb82c6777ccffd9e389c4a2837fe6f78c |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/friesian/example/dlrm/dlrm_preprocessing.py | Python | apache-2.0 | 6,611 | [
"ORCA"
] | 8ceda40053839978db43d171345b2ff1f995412c45d0f045765874a9bf894e2d |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
import os
class Orca(Package):
"""An ab initio, DFT and semiempirical SCF-MO package
Not... | iulian787/spack | var/spack/repos/builtin/packages/orca/package.py | Python | lgpl-2.1 | 2,751 | [
"ORCA"
] | 223deba023954c96334eba60bd277e459c6af56feec0d3b685b24f011264ffcd |
import tensorflow as tf
import numpy as np
from ops import *
from utils import *
import input_data
# from scipy.misc import imsave as ims
class Draw():
def __init__(self):
self.mnist = input_data.read_data_sets("MNIST_data/", one_hot=True)
self.n_samples = self.mnist.train.num_examples
se... | HaydenFaulkner/phd | tensorflow_code/external_libraries/draw-kvfrans/main.py | Python | mit | 9,552 | [
"Gaussian"
] | f19033d43b49e51fc230bf03179a1fe1226290f85a75b5d8aebfcb60410784aa |
__RCSID__ = "$Id $"
# We disable the no-member error because
# they are constructed by SQLAlchemy for all
# the objects mapped to a table.
# pylint: disable=no-member
import datetime
import errno
# # from DIRAC
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.DataManagementSystem.Client.FTS3Operation import FTS3Op... | Andrew-McNab-UK/DIRAC | DataManagementSystem/DB/FTS3DB.py | Python | gpl-3.0 | 16,779 | [
"DIRAC"
] | 787407bcb7970999908c5df1e90e1cce1b8e9298457c68b7489a6cfc37db7c7c |
##############################################################################
# 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... | tmerrick1/spack | var/spack/repos/builtin/packages/busco/package.py | Python | lgpl-2.1 | 2,734 | [
"BLAST"
] | a8254877606f321acc0c89aac6f5f60609f2031cfe74ea58376c44674eb6057c |
# 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... | FCP-INDI/nipype | nipype/interfaces/fsl/model.py | Python | bsd-3-clause | 88,336 | [
"Gaussian"
] | 48a325834f3bfd087f0048bcae2a8b9feabd580956ce923256e7ce0b634fcd25 |
"""
An example creating a structured grid data set from numpy arrays using TVTK
and visualizing it using mlab.
In this example, we create a structured-grid data set: we describe
data, both scalar and vector, lying on a structured-grid, ie a grid where
each vertex has 6 neighboors. For this we directly create a
Structu... | dmsurti/mayavi | examples/mayavi/mlab/simple_structured_grid.py | Python | bsd-3-clause | 2,224 | [
"Mayavi",
"VTK"
] | d48aa65e8f89cd639dc30d0a2352c4f2b59b1f543c99022eaa334a51eebe65f4 |
#-----------------------------------------------------------------------------
# Copyright (c) 2013-2014, Allen B. Riddell
#
# This file is licensed under Version 3.0 of the GNU General Public
# License. See LICENSE for a text of the license.
#----------------------------------------------------------------------------... | ariddell/horizont | setup.py | Python | gpl-3.0 | 6,222 | [
"VisIt"
] | 6a045ec9cc349f0443a996d1420f9a183538255256ac9b2d45640c50efcd3e78 |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio-Client.
# Copyright (C) 2014 CERN.
#
# Invenio-Client is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, or (at your opt... | inveniosoftware/invenio-client | invenio_client/connector.py | Python | gpl-2.0 | 18,756 | [
"VisIt"
] | d05b6c412f30249d39ec161941078f6c12c955f72ab157f4717f5c5316c20627 |
# Character.py
# Aaron Taylor
# Moose Abumeeiz
#
# This is the class for the main character it handles all controls and
# functions that they have
from pygame import *
from random import randint
from math import *
from const import GRATIO
from UIHeart import *
from Tear import *
from Fire import *
from Coin import *
f... | ExPHAT/binding-of-isaac | Character.py | Python | mit | 13,914 | [
"MOOSE"
] | 7da81593bc80f9abc7db9d713a111a01472e9b99c56b84ecabf2e98ba2556afe |
import os
import numpy as np
from ase import Atom, Atoms
from ase.lattice import bulk
from ase.units import Hartree, Bohr
from gpaw import GPAW, FermiDirac
from gpaw.response.bse import BSE
from ase.dft.kpoints import monkhorst_pack
from gpaw.mpi import rank
GS = 1
bse = 1
check = 1
if GS:
kpts = (4,4,4)
a ... | robwarm/gpaw-symm | gpaw/test/bse_silicon.py | Python | gpl-3.0 | 1,576 | [
"ASE",
"GPAW"
] | 0085673b9554f56d010ea9a19b92d77c511f2a36ad02bfeddac94a60b3a4d956 |
"""Module level constants specifying available data"""
from datetime import datetime as dt
MIN_SEASON = 2008
"""Oldest season currently supported"""
MAX_SEASON = dt.today().year if dt.today().month < 10 else dt.today().year + 1
"""Year of the most recent season. Seasons are denoted by the year in which they end, i.... | robhowley/nhlscrapi | nhlscrapi/constants.py | Python | apache-2.0 | 5,910 | [
"COLUMBUS"
] | 303554d5f60d8514ecc10312b54c2b963e5fdaf2016846b1234cfbef1130bdd4 |
# -*- coding: utf-8 -*-
from flask import Blueprint, render_template, request, redirect, flash, url_for
from flask.ext.login import login_required, current_user
from octopus.extensions import nav, db
from octopus.user.forms import EditUserProfile
from octopus.models import User
from octopus.utils import flash_errors
... | quaintm/octopus | octopus/user/views.py | Python | bsd-3-clause | 2,064 | [
"Octopus"
] | ad95e5202cda1fd0dd71786f251f0cb85ce131e67250b56234c8aa5143e22dbb |
# -*- coding: utf-8 -*-
# Copyright 2020 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | sasha-gitg/python-aiplatform | tests/unit/gapic/aiplatform_v1/test_endpoint_service.py | Python | apache-2.0 | 109,566 | [
"Octopus"
] | 26b9002fe4884b3a06faa6cc2ba5060a076eab6702a620436d98ddd4e6cd625f |
"""
Test topological fingerprints.
"""
import unittest
from rdkit import Chem
from deepchem.feat import fingerprints as fp
class TestCircularFingerprint(unittest.TestCase):
"""
Tests for CircularFingerprint.
"""
def setUp(self):
"""
Set up tests.
"""
smiles = 'CC(=O)O... | Agent007/deepchem | deepchem/feat/tests/test_fingerprints.py | Python | mit | 1,540 | [
"RDKit"
] | 81c858ccf0b9328c5317683653c0012b984f0b26c344eb17aa85cb11dd0a0934 |
""" Creates a class structure for optical elements
The key difference between an optical element and a ray matrix is that an
optical element can consist of several ray matrices which together act
as a single element. The most common example is that of a thick lens which
consists of two curved interfaces and an interv... | chrisark7/pylase | pylase/optical_element.py | Python | gpl-3.0 | 11,728 | [
"Gaussian"
] | 6f6ffc379275b5c063ab981637e1f000a1a2e74cf5c456cb8c54b8ebd19bbf72 |
# encoding: utf-8
from Tkinter import *
from itertools import izip
from functools import partial
from penview import *
class XYPlot(Canvas):
"a custom canvas to display xy-plots"
def __init__(self, parent, window, width, height):
self.canvas_color = "#eef"
# ouff
#
... | Pfiver/penview | graph_view.py | Python | gpl-3.0 | 20,879 | [
"FLEUR"
] | a0b40d58db9778c244dc9e95fcf5d5484794d393a16d09dafd74c3f73b5e19a1 |
#!/usr/bin/env python
import os
import sys
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot, vtkGetTempDir
gotWarning = False
gotError = False
def WarningCallback(obj, evt):
global gotWarning
gotWarning = True
VTK_DATA_ROOT = vtkGetDataRoot()
VTK_TEMP_DIR = vtkGetTempDir()
#... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/IO/Image/Testing/Python/TestPNGTextChunks.py | Python | gpl-3.0 | 3,519 | [
"VTK"
] | 4017112789883eddf64934663ea5363bf070b9fad3a27b8ee525daa57d586a78 |
tutorial_tests = """
Let's try a simple generator:
>>> def f():
... yield 1
... yield 2
>>> for i in f():
... print i
1
2
>>> g = f()
>>> g.next()
1
>>> g.next()
2
"Falling off the end" stops the generator:
>>> g.next()
Traceback (most recent call la... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-2.5/Lib/test/test_generators.py | Python | mit | 49,661 | [
"VisIt"
] | 0fc1cc0937ad13986c8b7a006db31cd81adf8c29e451bab78246d2394b298a13 |
# Author: Samuel Ponc\'e
# Date: 30/04/2013 -- 11/09/2014
# Version 1.3
# Classes needed for the temperature.py script
# Last devel info: Dynamical coding done
import numpy as N
from numpy import zeros
import itertools as Iter
from functools import partial
import multiprocessing
import netCDF4 as nc
import sys
import ... | jmbeuken/abinit | scripts/deprecated/rf_mods.py | Python | gpl-3.0 | 50,782 | [
"NetCDF"
] | 1f15c2eb92b00108328e2feafbc80c2c7c6b5ca1ea5e757dbf62e1f2787a8d33 |
#!/usr/bin/env python
from optparse import OptionParser
from ase.io import filetype
from ase.io.aff import print_aff_info
from ase.io.pickletrajectory import print_trajectory_info
from ase.io.bundletrajectory import print_bundletrajectory_info
description = 'Print summary of information from trajectory files.'
def ... | misdoro/python-ase | ase/cli/info.py | Python | gpl-2.0 | 957 | [
"ASE"
] | dd7002767c77ccd2fe3256c5d3b36887fc0a9bf245202523d23ebc2652183383 |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Deleting field 'EphysConceptMap.added_by_old'
db.delete_column('neuroelectro_ephysconceptmap', ... | neuroelectro/neuroelectro_org | neuroelectro/south_migrations/0052_auto__del_field_ephysconceptmap_added_by_old__del_field_neuronephysdat.py | Python | gpl-2.0 | 27,484 | [
"NEURON"
] | a25655366b89871dc12c9e7cffa0f90ace9ed8c0f8a023bfcddb37cfc9523f42 |
"""Plots spatially subset model evaluation."""
import os.path
import warnings
import argparse
import numpy
import matplotlib
matplotlib.use('agg')
from matplotlib import pyplot
from mpl_toolkits.basemap import Basemap
from generalexam.ge_utils import utils as ge_utils
from gewittergefahr.gg_utils import general_utils
... | thunderhoser/GewitterGefahr | gewittergefahr/scripts/plot_spatially_subset_eval.py | Python | mit | 23,603 | [
"Gaussian"
] | ed41fcdd176b150b301a5379677425ff76b8b4abd8aad63598c8ff994bbe6384 |
'''
This __init__ file is for a PySCeS "eXtension module" (pysx), the following variables can be set for each module
'''
pysx_name = 'PySCeS SBW interface'
pysx_oscompat = ['nt']
pysx_base_class = 'CONTRIB_sbw'
pysx_author = 'Herbert Sauro et al.'
pysx_email = ''
pysx_affiliation = 'Kegg Graduate Institute'
pysx_web =... | asttra/pysces | pysces/contrib/sbw/__init__.py | Python | bsd-3-clause | 439 | [
"PySCeS"
] | 417e867a44881ceb02e14915548535134b5fb11901cfe4cf1f1eac02ce662b30 |
__doc__="""Optimal photometry, for one faint star and one bright reference star.
Optimised for timeseries creation. Data variables are module wide.
optext: runs the routine"""
from Scientific.Functions.LeastSquares import leastSquaresFit as LS
#fitting data (used but not changed in functions)
FWHM = 3.
inannmult = 2... | martindurant/astrobits | optext.py | Python | mit | 2,700 | [
"Gaussian"
] | fc20d799d79a2f56629f2ab3f337a3d639f126384c12b5598bdb6d46f19449b4 |
# OpenRTS - Copyright (C) 2006 The OpenRTS Project
#
# OpenRTS is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# OpenRTS is distribu... | Donkyhotay/openrts | client/mainmenu.py | Python | gpl-2.0 | 5,932 | [
"VisIt"
] | cc915d0d526a27833adbfcb74966bad9776314b76aaf156dde6d4d154d8eb4a2 |
# -*- coding: utf-8 -*-
''' Display nice images of the model. '''
__author__= "Luis C. Pérez Tato (LCPT) , Ana Ortega (AO_O) "
__copyright__= "Copyright 2016, LCPT, AO_O"
__license__= "GPL"
__version__= "3.0"
__email__= "l.pereztato@ciccp.es, ana.ortega@ciccp.es "
import sys
import vtk
import xc_base
import geom
fr... | lcpt/xc | python_modules/postprocess/xcVtk/vtk_graphic_base.py | Python | gpl-3.0 | 10,495 | [
"VTK"
] | 49e70010f8a2f45cb57d79a9080c4cddce2305151f53f275eab0758fffb054e8 |
"""This is the homerwork for CS8803 ASE
implemented using Google Cloud Endpoints.
Defined here are the ProtoRPC messages needed to define Schemas for methods
as well as those methods defined in an API.
"""
import sys
sys.path.insert(0, 'lib')
import webapp2
import string
from textblob import TextBlob
from textblob.se... | nelango/ViralityAnalysis | model/predictor.py | Python | mit | 10,218 | [
"ASE"
] | c2c46e5fd65a20185bba25cf45d423c9d5334a0d5d56a92e89779d70a14b1acf |
# Copyright 2001 by Gavin E. Crooks. 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.
""" Handle the SCOP DEScription file.
The file format is described in the scop
"release no... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/SCOP/Des.py | Python | apache-2.0 | 3,692 | [
"Biopython"
] | 2d5cba190d44d6690ac279492525a38d64c78d5aca53d7389b9cf7d345b9e839 |
#!/usr/bin/python
##This Python file uses the following encoding: utf-8
##
## (C) 2015 Muthiah Annamalai,
## Licensed under GPL Version 3
##
## Module has elements of PARSE-TREE AST and generates
## a Graphviz file for the AST. WIP.
##
import codecs
import functools
import sys
import xml
from .ezhil_sca... | arcturusannamalai/Ezhil-Lang | ezhil/ezhil_visualizer.py | Python | gpl-3.0 | 12,640 | [
"VisIt"
] | 3914da63c70c65394655b6319cde7e63ee9ff10ab3eb6a6029c55fdd9dc4d33f |
"""
################################################################################
#
# SOAPpy - Cayce Ullman (cayce@actzero.com)
# Brian Matthews (blm@actzero.com)
# Gregory Warnes (Gregory.R.Warnes@Pfizer.com)
# Christopher Blunck (blunck@gst.com)
#
##########################... | cmsdaq/hltd | lib/SOAPpy-py3-0.52.24/src/SOAPpy/Server.py | Python | lgpl-3.0 | 26,981 | [
"Brian"
] | 5ae144fb83e328c88cb8654ba646880f50f9d3dd8b3d5116eb59ac6d437dd567 |
##
# Copyright 2009-2015 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# the Hercules foundation (htt... | ULHPC/modules | easybuild/easybuild-easyblocks/easybuild/easyblocks/w/wien2k.py | Python | mit | 18,274 | [
"WIEN2k"
] | 73e6783c478058a3ab7fe3eeb9e555378fc82f89638e3778994d5463b325d438 |
from .posterior import Posterior
from ...util.linalg import jitchol, tdot, dtrtrs, dtrtri, pdinv
from ...util import diag
import numpy as np
from . import LatentFunctionInference
log_2_pi = np.log(2*np.pi)
class PEP(LatentFunctionInference):
'''
Sparse Gaussian processes using Power-Expectation Propagation
... | befelix/GPy | GPy/inference/latent_function_inference/pep.py | Python | bsd-3-clause | 3,521 | [
"Gaussian"
] | 2b611ccb6e7ff5b0aca0b0e98539815ee1cd0a39310c271ccf071262107a21e4 |
# -*- coding: utf-8 -*-
# GromacsWrapper
# Copyright (c) 2009 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
from __future__ import division, absolute_import, print_function
import pytest
from numpy.testing import assert_equ... | Becksteinlab/GromacsWrapper | tests/fileformats/test_convert.py | Python | gpl-3.0 | 2,029 | [
"Gromacs"
] | 14f477a227e1db3335cb1cb024abe61aa0b0b060c1626dbd452db01dbb10dc32 |
# -*- coding: utf-8 -*-
# Copyright 2013 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
from urllib.request import urlopen
import unittest
from splinter import Browser
from .fake_webapp import EXAMPLE_APP
from .base import... | cobrateam/splinter | tests/test_webdriver_remote.py | Python | bsd-3-clause | 1,813 | [
"VisIt"
] | 4c8f48e9bd49b497493a03032907d0c67ff937eac6adaf66415b4ffcf8b43c49 |
import pymol
from pymol import stored
from pymol import cmd, CmdException
cmd=pymol.cmd
input_file='4oe9.pdb'
cmd.load( input_file , '4oe9' )
| S-John-S/MAT | sb_script.py | Python | mit | 144 | [
"PyMOL"
] | ab3fc5e42c6ecb9c868be7edabb3394a640fb12098fc3255179c7bdef82f844e |
__author__ = 'noe'
import unittest
import numpy as np
import time
from bhmm import hidden
from bhmm.output_models.gaussian import GaussianOutputModel
print_speedup = False
class TestHidden(unittest.TestCase):
def setUp(self):
self.nexamples = 0
self.A = []
self.pi = []
sel... | bhmm/legacy-bhmm-force-spectroscopy-manuscript | bhmm/tests/test_hidden.py | Python | lgpl-3.0 | 13,255 | [
"Gaussian"
] | 400f611053b5bb4bf57826dfe74712f875e8fca40d649eed028ac47a8fdc9e88 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkXMLStructuredGridReader(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkXMLStructuredGridReader.py | Python | bsd-3-clause | 520 | [
"VTK"
] | 9d6662f240b09233b832cde1c3b728908844667f6d7022e14b2fe13f2a6bf5eb |
"""An NNTP client class based on RFC 977: Network News Transfer Protocol.
Example:
>>> from nntplib import NNTP
>>> s = NNTP('news')
>>> resp, count, first, last, name = s.group('comp.lang.python')
>>> print 'Group', name, 'has', count, 'articles, range', first, 'to', last
Group comp.lang.python has 51 articles, rang... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-2.2/Lib/nntplib.py | Python | mit | 18,773 | [
"Brian"
] | 2adeba1d1654ddc6be86d9afcc62487ed0d1c1e87542efb6dc570e41709431bd |
""" Test class for JobWrapper
"""
#pylint: disable=protected-access, invalid-name
# imports
import unittest
import importlib
import os
import shutil
from mock import MagicMock, patch
from DIRAC import gLogger
from DIRAC.DataManagementSystem.Client.test.mock_DM import dm_mock
from DIRAC.Resources.Catalog.test.mock_... | andresailer/DIRAC | WorkloadManagementSystem/JobWrapper/test/Test_JobWrapper.py | Python | gpl-3.0 | 4,402 | [
"DIRAC"
] | 3c53fe8c691471697a1c1e625aeccfc2fa266754588c0fae51776a34d060f2a8 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# nettest_nodes - [insert a few words of module description on this line]
# Copyright (C) 2003-2011 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 te... | heromod/migrid | mig/grsfs-fuse/fs/nettest_nodes.py | Python | gpl-2.0 | 3,508 | [
"Brian"
] | 010e9a2deb930e2488723a479ffcf26a5e6a96446114a8e78781c7f87a6a8602 |
"""Provide analysis of input files by chromosomal regions.
Handle splitting and analysis of files from chromosomal subsets separated by
no-read regions.
"""
import collections
import os
import toolz as tz
from bcbio import utils
from bcbio.distributed.split import parallel_split_combine
from bcbio.pipeline import da... | biocyberman/bcbio-nextgen | bcbio/pipeline/region.py | Python | mit | 7,498 | [
"Galaxy"
] | 6f66013cccbfd84543d54e974909d4586cd909405e3c600ac952cf7d4527bd02 |
# 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... | tntnatbry/tensorflow | tensorflow/tools/common/public_api.py | Python | apache-2.0 | 3,732 | [
"VisIt"
] | d94a342842fa458fe4cedd923cca4e2c55345a526749e0c28b8fe6c0bde47581 |
import numpy as np
from gpaw.utilities.blas import gemm
from gpaw.utilities import pack, unpack2
from gpaw.utilities.timing import nulltimer
class EmptyWaveFunctions:
def __nonzero__(self):
return False
def set_eigensolver(self, eigensolver):
pass
def set_orthonormalized(self, flag)... | qsnake/gpaw | gpaw/wavefunctions/base.py | Python | gpl-3.0 | 15,178 | [
"GPAW"
] | 5744ee2da0a391883b4cb8ced5ea4fac563223764552c9dbb885e7f99912c66a |
import caching.base as caching
import jingo
import jinja2
from tower import ugettext_lazy as _
import amo
from addons.models import Addon
from api.views import addon_filter
from bandwagon.models import Collection, MonthlyPick as MP
from versions.compare import version_int
# The global registry for promo modules. Ma... | magopian/olympia | apps/discovery/modules.py | Python | bsd-3-clause | 11,312 | [
"VisIt"
] | a0b1c6e429f280d0c02d05b61dea5e4bb9c1c48baceaec4bf86858c66f394430 |
# Copyright (c) 2013-2015 Siphon Contributors.
# Distributed under the terms of the BSD 3-Clause License.
# SPDX-License-Identifier: BSD-3-Clause
"""
================
NCSS and CartoPy
================
Use Siphon to query the NetCDF Subset Service (NCSS) and plot on a map.
This example uses Siphon's NCSS class to prov... | Unidata/siphon | examples/ncss/NCSS_Cartopy_Example.py | Python | bsd-3-clause | 4,735 | [
"NetCDF"
] | 6fae6a0a92a598c014be10475ceb2738722488320d64fae9f992b9d19feb2615 |
## Propulsion.py
## Problems and solutions in Propulsion
######################################################################################
## Copyleft 2015, Ernest Yeung <ernestyalumni@gmail.com>
## 20151112
... | ernestyalumni/Propulsion | Propulsion.py | Python | gpl-2.0 | 11,699 | [
"Avogadro"
] | e32ae895665f769bac6e98c68c78ad6d779e9ffb7715e7e9d275605e640a35ed |
#!/usr/bin/env python
# ======================================================================
# Globally useful modules, imported here and then accessible by all
# functions in this file:
import numpy,atpy,sys,getopt,string,subprocess,pyfits
import localgroup
# It would be nice to read in tables from FITS, but I c... | drphilmarshall/LocalGroupHaloProps | attic/LGweights.py | Python | gpl-2.0 | 25,885 | [
"Galaxy"
] | 304ac96825621850b986463480dface463444aa9014fd6830b8012c0583005c6 |
#
# Copyright (C) 2013-2018 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | hmenke/espresso | testsuite/python/particle.py | Python | gpl-3.0 | 10,814 | [
"ESPResSo"
] | bdf3c9f6e0ab3934bcff453ad54027e836d0dd1a0b2d76a37160adaf7cfcdf86 |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, print_function
import tensorflow as tf
from niftynet.layer.base_layer import Layer
from niftynet.layer.fully_connected import FullyConnectedLayer
from niftynet.layer.convolution import ConvolutionalLayer
from niftynet.utilities.util_common import look_up... | NifTK/NiftyNet | niftynet/layer/squeeze_excitation.py | Python | apache-2.0 | 4,408 | [
"exciting"
] | bd56d0e85544f706d58cc5a29f6073e3b6efbd3bacf472c8db20d21a592862ee |
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; either version 2 of the License, or (at your option) any later
# version.
#
# This program is distributed in the hope that it will be useful, but ... | shaleh/clonedigger | clonedigger/logilab/astng/inspector.py | Python | gpl-3.0 | 9,335 | [
"VisIt"
] | f1775240b8ae862785e53eb623f378ff0bfbd87ec37428b8fc815e9eab107053 |
#!/usr/bin/env python
#-*- coding:utf-8 -*-
# test_attributes.py
"""
Test the validity of graph, node, and edge attributes as well as the
distribution generators.
"""
import os
import unittest
import numpy as np
import pytest
import nngt
from base_test import TestBasis, XmlHandler, network_dir
from tools_testing... | Silmathoron/NNGT | testing/test_attributes.py | Python | gpl-3.0 | 13,217 | [
"Gaussian"
] | a89a8c3bc01eca7c44a31a75ae6485ecd79450c8ffc4aca27f55df52cdff7cb7 |
#!/usr/bin/env python3
import sys
import multiprocessing
from pathlib import Path
import jinja2
import pypandoc
import pytoml as toml
from common import validate_toml, get_tt_version
if (sys.version_info.major, sys.version_info.minor) < (3, 6):
raise Exception("need Python 3.6 or later")
THIS_FILE = Path(__fil... | monome/teletype | utils/cheatsheet.py | Python | gpl-2.0 | 4,577 | [
"ORCA"
] | ada6ccd75645439447316f3d519abbaf351321ad3ddd873a82bfbae87b43cb04 |
""" A module with Gaussian functions for creating Gaussian distributions
in 1D, 2D and 3D. There are also functions with the same name and _FIT
which can be used to fit an intensity distribution in a ndarray with the
corresponding Gaussian distribution using scipy's curve_fit.
A 1D Lorentz and a 1D gaussLorentz functi... | ercius/openNCEM | ncempy/algo/gaussND.py | Python | gpl-3.0 | 17,632 | [
"Gaussian"
] | e4a53a6282b22007e18da741d19ad0aac853a7df8bfb006e6ffd617e3217e007 |
#!/usr/bin/env python
##This Python file uses the following encoding: utf-8
##
## (C) 2017 Muthiah Annamalai,
## XML
from __future__ import print_function
from xml.dom.minidom import parse
import sys
import os
import tamil
import codecs
import re
import pprint
from xml.dom.minidom import parse as xml_parse
from xml.do... | arcturusannamalai/Ezhil-Lang | editor/DocView.py | Python | gpl-3.0 | 13,991 | [
"VisIt"
] | aba87f23b3e80a3886e6ffd91bd06fe46dace4b568c1a6084fe311b4feb0265e |
# coding=utf-8
# Copyright 2022 The Uncertainty Baselines Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ap... | google/uncertainty-baselines | baselines/diabetic_retinopathy_detection/rank1_bnn.py | Python | apache-2.0 | 22,076 | [
"Gaussian"
] | a6f21e4b5ddb2bcf1e277684311ce0e66313de2119e055ebed8e7f9231ed32af |
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/normal_chr04.py | Python | mit | 25,843 | [
"MCell"
] | d23fe98df6ad27851e55e2688b39b5a3c8463b90cf561b19617eee9cb69b9286 |
""" Some utilities for FTS3...
"""
import json
import datetime
import random
import threading
from DIRAC.DataManagementSystem.Client.DataManager import DataManager
from DIRAC.FrameworkSystem.Client.Logger import gLogger
from DIRAC.Core.Utilities.Decorators import deprecated
from DIRAC.Core.Utilities.ReturnValues impo... | arrabito/DIRAC | DataManagementSystem/private/FTS3Utilities.py | Python | gpl-3.0 | 12,089 | [
"DIRAC"
] | 845dc95f6090d2e217194447f8b7c297cbdcc7954870fff5160da9a9c9500732 |
# This script is executed in the main console namespace so
# that all the variables defined here become console variables.
import ddapp
import os
import sys
import PythonQt
import json
from PythonQt import QtCore, QtGui
from time import time
import imp
import ddapp.applogic as app
from ddapp import drcargs
from ddapp... | edowson/director | src/python/ddapp/startup.py | Python | bsd-3-clause | 37,735 | [
"VTK"
] | 2d44a3a7a64e7ce63b7b34c098246c4bf640e877bd93bad73dfce5337b77ddd6 |
import os
import sys
import argparse
import roblib
__author__ = 'Rob Edwards'
def read_blast_file(filename, query=True, evalue=10, bitscore=0):
"""
Read the blast output file and return a dict of hits that has contig, start, stop.
# crAssphage_C NODE_1_length_14386_cov_54.5706_ID_1703 94.64 1157 6... | linsalrob/EdwardsLab | blast/blast_to_sequences.py | Python | mit | 4,322 | [
"BLAST"
] | c379d34121aa7607c7cf5be12ebff6a0cdb34bc48175f5663eff74037869bed5 |
#!/usr/bin/env python
########################################################################
# File : dirac-proxy-init.py
# Author : Adrian Casajus
########################################################################
import os
import sys
import glob
import time
import datetime
import DIRAC
from DIRAC import ... | andresailer/DIRAC | FrameworkSystem/scripts/dirac-proxy-init.py | Python | gpl-3.0 | 11,024 | [
"DIRAC"
] | b9a82f417ad5cbe8c62c51a5ed8384763fd7b9360dd0c457772b6239d4eff790 |
# detection anomalies from SDSS using global PCA method
from ex import *
from feature import GetFeatures
import sdss_info as sinfo
from detector import *
import report
def usage():
print('''
get the anomaly scores using global pca method
python --feature --scorer [--nproc={number of parallel processes}]
''')
... | excelly/xpy-ml | sdss/detection/detection_point.py | Python | apache-2.0 | 1,920 | [
"Galaxy"
] | a6de0e1687a3a314a9ba541ab0f011055fe03bc08191aa1924425974e896f118 |
#!/usr/bin/python
"""This script run the orf prediction """
try:
import sys, re, csv, traceback
from os import path, _exit, rename
import logging.handlers
from optparse import OptionParser, OptionGroup
from libs.python_modules.utils.sysutil import pathDelim
from libs.python_modules.utils.metapathwa... | wholebiome/MetaPathways_Python_Koonkie.3.0 | libs/python_scripts/MetaPathways_func_search.py | Python | mit | 8,808 | [
"BLAST"
] | 6f03825d20515ad6a9b86a009566ea32ca590b98fce3a12324f27896d8278098 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Create the RenderWindow, Renderer and both Actors
#
ren1 = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren1)
iren = vtk.vtkRenderWindowInteractor(... | timkrentz/SunTracker | IMU/VTK-6.2.0/Filters/Texture/Testing/Python/socbal.py | Python | mit | 13,848 | [
"VTK"
] | f9ff96e343b6888b2b3a49e408d93ee025188f8723f24304d0524d8ae2778cac |
import itertools
import collections
import numpy as np
#=======================================================================================================================================================================
# GROMACS Specific Definitions
#==... | fgrunewald/Martini_PolyPly | polyply/itp_tool/itp_I.py | Python | gpl-3.0 | 18,100 | [
"Gromacs"
] | 35cb5b178337794fd8bc69f21ac092a27e38617c5195f371e5ec2cdda6f998d9 |
# coding=utf-8
from __future__ import unicode_literals
from collections import OrderedDict
from .. import Provider as PersonProvider
class Provider(PersonProvider):
formats = (
'{{first_name_male}} {{last_name}}',
'{{first_name_male}} {{last_name}}',
'{{first_name_male}} {{last_name}}',
... | Nebucatnetzer/tamagotchi | pygame/lib/python3.4/site-packages/faker/providers/person/en_GB/__init__.py | Python | gpl-2.0 | 18,349 | [
"Amber",
"Brian"
] | 152817814d03c281acde134d7e95b25f6a404bcc5bc2cfc89086ecc7a95a43a6 |
import glob
import inspect
import logging
import os
from flask import jsonify, Blueprint, request
from kalliope.core.ResourcesManager import ResourcesManager, ResourcesManagerException
from kalliope.core.Utils import Utils
logging.basicConfig()
logger = logging.getLogger("kalliope")
LIST_EXCLUDED_DIR_NAME = ["__pyca... | kalliope-project/kalliope | kalliope/core/RestAPI/views/neurons_view.py | Python | gpl-3.0 | 4,175 | [
"NEURON"
] | 4ffd2ed78bc3559caaaeb41b8b6a896f1b6242b030608a8d1d7c99cd2c7586c4 |
"""Tests for visit tracking middleware."""
# pylint: disable=invalid-name
from django.conf import settings
from django.contrib.auth import get_user_model
from django.core.urlresolvers import reverse
from django.test import TestCase, RequestFactory
from django.test.utils import override_settings
from mock import Mock
f... | ofa/connect | open_connect/middleware/tests/test_visit_tracking.py | Python | mit | 3,298 | [
"VisIt"
] | 4480d4a7d94cdcc53b42736bcfa11f16c90dc8ce8afafc90c042206988739729 |
#* 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 peacoc... | nuclear-wizard/moose | python/peacock/utils/ExeLauncher.py | Python | lgpl-2.1 | 1,932 | [
"MOOSE"
] | 7500fc09fdfa32c29070759ee17eef0f4b43068936f7e094bfc9fe645be603cd |
# coding: utf-8
import unittest
import numpy as np
import neurolab as nl
import numpy.random as rand
class TestNet(unittest.TestCase):
def test_newp(self):
# Logical &
input = [[0, 0], [0, 1], [1, 0], [1, 1]]
target = [[0], [0], [0], [1]]
# Create net with 2 inputs and 1 neuron... | blagasz/python-ann | neurolab/test/net.py | Python | gpl-2.0 | 4,705 | [
"NEURON"
] | c2a6647ef4b21089e81f8a058af5834394f6089626d3bc22acf03d1996072934 |
#!/usr/bin/env python
import re,sys
def get_mRNA(fold_data,speed_scores):
rna_seq = []
for datum in fold_data:
#get rna for segment that was crystalised
seg_start = int(datum.rna_aligned_start) - (int(datum.protein_aligned_start)-1)*3 - 1
seg_end = seg_start + len(datum.protein_sequence)*3
rna = datum.rna... | Alicimo/codon_optimality_code | working_directory/mRNA.py | Python | gpl-2.0 | 1,821 | [
"CRYSTAL"
] | 992f68f5f36be47ad7ce48d60932548175c479368f16293b27aa1e392156ee0c |
#!/usr/bin/env python
"""
Script that facilitates the modification of a element through the command line.
However, the usage of this script will set the element token to the command
issuer with a duration of 1 day.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_f... | yujikato/DIRAC | src/DIRAC/ResourceStatusSystem/scripts/dirac_rss_set_status.py | Python | gpl-3.0 | 8,531 | [
"DIRAC"
] | ddf6632f963f6f2a831db264ca3abee2658588378ef8348b84cefc80d8bd2c9d |
"""
DataFrame
---------
An efficient 2D container for potentially mixed-type time series or other
labeled data series.
Similar to its R counterpart, data.frame, except providing automatic data
alignment and a host of useful data manipulation methods having to do with the
labeling information
"""
from __future__ import... | gfyoung/pandas | pandas/core/frame.py | Python | bsd-3-clause | 369,149 | [
"Elk"
] | 3a2458d5bc79666dde7b1d06098b40069337dd441fa91a7ed60aae3780a88881 |
#!/usr/bin/python
"""
Copyright 2012 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester 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 th... | clreinki/GalaxyHarvester | postRecipe.py | Python | agpl-3.0 | 10,852 | [
"Galaxy"
] | 4854eae057079c6e11aed43feee0a154f3c33168d8d89a58e9823a76ca77d36b |
#
# 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... | jbonofre/beam | sdks/python/apache_beam/examples/snippets/snippets.py | Python | apache-2.0 | 43,029 | [
"VisIt"
] | 88f7234e758d1a68b644292fa8dcb9ce2c2538b54ca1dca5a7581ef96f210ca3 |
########################################################################
# File: FTSFileTests.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/04/16 06:45:16
########################################################################
""" :mod: FTSFileTests
==================
.. module: FTSFileTests
:s... | andresailer/DIRAC | DataManagementSystem/Client/test/Test_FTSFile.py | Python | gpl-3.0 | 2,034 | [
"DIRAC"
] | 8ac18c79264f45a3085a1013565242d83d9c4f29e050dc841de78727f12fc327 |
# HsolveInstability.py ---
# Commentary:
#
# A toy compartmental neuronal + chemical model in just a cubic volume
#
# 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 3, or
# (a... | dilawar/moose-full | moose-examples/snippets/cubeMeshSigNeur.py | Python | gpl-2.0 | 11,878 | [
"MOOSE"
] | c7de3684afe6793d8792648dcead33533570d8b834937215ebd430b87a0c585e |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | modules/tensor_mechanics/test/tests/capped_mohr_coulomb/small_deform_15_16_17.py | Python | lgpl-2.1 | 1,765 | [
"MOOSE"
] | 0874ad2cd7c93b0262363f15ed3f9ec07f600845f6ad0803f120ea8ec5cfb5b1 |
import logging
import numpy as np
import mdtraj as mdj
from wepy.reporter.reporter import ProgressiveFileReporter
from wepy.util.mdtraj import json_to_mdtraj_topology, mdtraj_to_json_topology
from wepy.util.json_top import json_top_subset
class WExploreAtomImageReporter(ProgressiveFileReporter):
"""Reporter for... | ADicksonLab/wepy | src/wepy/reporter/wexplore/image.py | Python | mit | 4,448 | [
"MDTraj",
"VMD"
] | 9bb34f13731337cf65dac5e26eac77cc390291e967cc03d942e2f1bb0a1a4d46 |
#This is a program that handles the actual image processing and
#answer detection. We are going to build mobile apps based on this
#program and hopefully we will be able to add more functionality to it.
import cv2
import numpy as np
def rectify(h):
h = h.reshape((4,2))
hnew = np.zeros((4,2),dtype = np.float32)... | HuimingCheng/AutoGrading | learning/edge_detection.py | Python | mit | 18,708 | [
"Gaussian"
] | 9a519b639cfccfc0ab50423eecf202cb4159e1db9b17c8fc7f86a470d71a537a |
#!/usr/bin/env python
"""Run a Gene Ontology Enrichment Analysis (GOEA), plots, etc.
Nature 2014_0126;
Computational analysis of cell-to-cell heterogeneity
in single-cell RNA-sequencing data reveals hidden
subpopulations of cells
http://www.nature.com/nbt/journal/v33/n2/full/nbt.3102.html#method... | lileiting/goatools | tests/test_nbt3102.py | Python | bsd-2-clause | 19,531 | [
"Bioconductor"
] | 08a258c01b82f264f487f1583f8d2e28bb9a74bf0ad7e97440708e6b0449b49c |
#!/usr/bin/env python
# Copyright 2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless... | gkc1000/pyscf | pyscf/qmmm/mm_mole.py | Python | apache-2.0 | 2,953 | [
"PySCF"
] | e9b98614bad5d95142477b98176343c694ae4a5a56966f505ba45d9d9c7d9fe6 |
import logging
import random
import numpy as np
from ray.rllib.agents import with_common_config
from ray.rllib.agents.dreamer.dreamer_torch_policy import DreamerTorchPolicy
from ray.rllib.agents.trainer_template import build_trainer
from ray.rllib.execution.common import STEPS_SAMPLED_COUNTER, \
LEARNER_INFO, _ge... | robertnishihara/ray | rllib/agents/dreamer/dreamer.py | Python | apache-2.0 | 8,884 | [
"Gaussian"
] | c940d69f6a3fafb5d47189697ad18184a74a9e77c710232efae0cc4fb718c5d5 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# (c) 2015, Brian Coca <bcoca@ansible.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
... | ravibhure/ansible | lib/ansible/modules/notification/jabber.py | Python | gpl-3.0 | 4,343 | [
"Brian"
] | f6a92254c79ffbe39deb691e2372c37ebe15800d83924f3780b5dbcc9db4fb72 |
# Embedded file name: /usr/lib/enigma2/python/Components/Converter/pliExpertInfo.py
from enigma import iServiceInformation, eServiceCenter, iPlayableService, iPlayableServicePtr
from Components.Converter.Converter import Converter
from Components.Element import cached
from Components.config import config
from Tool... | kingvuplus/boom | lib/python/Components/Converter/pliExpertInfo.py | Python | gpl-2.0 | 21,895 | [
"Galaxy"
] | d84c28fa116aac026b3c46944424f3c6dfc26faf08347c0410cab7c8a0157866 |
"""
################################################################################
#
# SOAPpy - Cayce Ullman (cayce@actzero.com)
# Brian Matthews (blm@actzero.com)
# Gregory Warnes (gregory_r_warnes@groton.pfizer.com)
# Christopher Blunck (blunck@gst.com)
#
###################... | intip/da-apps | plugins/da_centrallogin/modules/soappy/SOAPpy/Errors.py | Python | gpl-2.0 | 3,014 | [
"Brian"
] | 872ec02e6670b01b74172de0811e2727b0a1e40ff2e9338420babfb239a2459d |
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