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#
#@BEGIN LICENSE
#
# uhfno by Psi4 Developer, a plugin to:
#
# PSI4: an ab initio quantum chemistry software package
#
# 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 Li... | lothian/uhfno | __init__.py | Python | gpl-2.0 | 1,146 | [
"Psi4"
] | 08c71e0322cdeaa3e02703685375c136127246f0cf7de955e067e74530161fe8 |
# encoding: utf-8
"""
A simple utility to import something by its string name.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD License. The full license is... | mattvonrocketstein/smash | smashlib/ipy3x/utils/importstring.py | Python | mit | 1,485 | [
"Brian"
] | 19b81c67b492886bcb691cf6d74b42960453a7d88653e3fa0215b1d7b5eaac18 |
from rdkit import Chem
from rdkit import rdBase
from rdkit import RDConfig
import os
from rdkit.Chem import rdMolDescriptors as rdMD
from rdkit.Chem import AllChem
haveDescrs3D = hasattr(rdMD,'CalcAUTOCORR3D')
import time,unittest
def _gen3D(m,is3d,calculator):
if not is3d:
m = Chem.AddHs(m)
ps ... | rvianello/rdkit | Code/GraphMol/Descriptors/Wrap/test3D.py | Python | bsd-3-clause | 4,384 | [
"RDKit"
] | b1fa1e8457a0c071912ee4469c1580f4c94113096f1ac92343a406732058c1ba |
""" X509Chain is a class for managing X509 chains with their Pkeys
"""
__RCSID__ = "$Id$"
import os
import stat
import tempfile
import hashlib
import random
import binascii
from GSI import crypto
from DIRAC import S_OK, S_ERROR
from DIRAC.Core.Utilities import DErrno
from DIRAC.Core.Security.pygsi.X509Certificate im... | fstagni/DIRAC | Core/Security/pygsi/X509Chain.py | Python | gpl-3.0 | 22,605 | [
"DIRAC"
] | b554a550c7438481fecb18663ea09cd187a4e7ad833869842c058ba72c0829b8 |
##
# Copyright 2013-2020 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://www.vscentrum.be),
# Flemish Research Foundation (F... | pescobar/easybuild-easyblocks | easybuild/easyblocks/c/charmm.py | Python | gpl-2.0 | 6,324 | [
"CHARMM",
"GAMESS",
"Gaussian",
"Q-Chem"
] | 183e469a044637c5cb738ec813eead2bfb3ebf03228d2677db70b16a63d0f829 |
from .utils import calc_uvb, calc_local_jnu, read_starburst99, get_data_path,\
tilt_spec, find_gamma
from barak.utilities import adict, between
from barak.constants import Ryd, Ryd_Ang, pi, hplanck
from barak.io import saveobj, parse_config, writetable
import numpy as np
from collections import OrderedDict
from... | nhmc/cloudy | run_and_parse.py | Python | bsd-3-clause | 25,419 | [
"Galaxy"
] | 224e1d4ca36ec81dfa17ef03a103abe3ab706592c235e80900891e3c90fa90fd |
r"""
Module handling kernel models in yaplf
Module :mod:`yaplf.models.kernel` contains all the classes handling kernel
models in yaplf.
AUTHORS:
- Dario Malchiodi (2010-02-15): initial version
"""
#*****************************************************************************
# Copyright (C) 2010 Dario Malchi... | dariomalchiodi/yaplf | yaplf/models/kernel.py | Python | lgpl-3.0 | 25,072 | [
"Gaussian"
] | b7a9f63fbdc38f4e4a397b8814b61db8de88698223cbf14244c8724d46687016 |
import os
import eva
import eva.base.adapter
import eva.job
import eva.exceptions
import eva.template
class FimexFillFileAdapter(eva.base.adapter.BaseAdapter):
"""
This adapter is a ``ncfill``, and in turn, FIMEX frontend that will fill a
NetCDF template file with GRIB or NetCDF data from other files. It... | metno/EVA | eva/adapter/fimex_fill_file.py | Python | gpl-2.0 | 5,892 | [
"NetCDF"
] | 6a5a9c58cd6f012e3fd4fe50215afb2310daaf5a06896d083ab5bf25b87e47b5 |
#!/usr/bin/python2
import sys
import errno
import glob
from Bio import SeqIO
# Daniel Elsner
# This script concatenates single alignments. Make sure there are no spelling errors in the sequence names. Only the alignment files to combine may be in the directory.
# Possibility to improve this, if necessary: Give also... | dewuem/python-bioinf | concatenate_alignments_flexible.py | Python | mit | 1,763 | [
"Biopython"
] | e980147893a5577a91b11d0d7c993555c1789cc15fea93d1a4a75478e46fc1be |
#!/usr/local/bin/python
"""Returns the age in hours of the oldest file in a directory hierachy.
This should work with munin-node (Unix) and munin-node32 (MS Windows)
Created 2008-11-12 by Maximillian Dornseif
"""
import sys
import os
import os.path
import time
def ltrim(text, length=29, replacement='...'):
"""... | mdornseif/hd-munin-plugins | oldestfile.py | Python | bsd-2-clause | 2,961 | [
"VisIt"
] | de7fc5edb0001442b55a85e750b20f1c177185412f36364142eb855f50753b96 |
import sys
from subprocess import Popen, PIPE
from mne.utils import run_tests_if_main
run_script = """
from __future__ import print_function
import sys
import mne
out = []
# check scipy
ok_scipy_submodules = set(['scipy', 'numpy', # these appear in old scipy
'fftpack', 'lib', 'linalg',... | teonlamont/mne-python | mne/tests/test_import_nesting.py | Python | bsd-3-clause | 1,697 | [
"Mayavi"
] | 4b370b621246a1cb604ecdce81087079e9a07f54b24743522d32bb0dd53238df |
#
# This source file is part of appleseed.
# Visit http://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2016 Haggi Krey, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of... | haggi/appleseed-maya | module/scripts/appleseed_maya/aetemplate/aeasdisneymaterialtemplate.py | Python | mit | 3,358 | [
"VisIt"
] | c6b84c887b5a87fbeeba501106b6464fc4b89a84cd729ea0747be207f019894c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforgecontrib/simulation/channels/inftauinterpolated/core.py | Python | bsd-2-clause | 3,223 | [
"NEURON"
] | 8b586779d4991a57cf04fef3f84e5dcad812ced020b21d61e468f178f5c412c6 |
"""Soundex algorithm
This program is part of "Dive Into Python", a free Python book for
experienced programmers. Visit http://diveintopython.org/ for the
latest version.
"""
__author__ = "Mark Pilgrim (mark@diveintopython.org)"
__version__ = "$Revision: 1.2 $"
__date__ = "$Date: 2004/05/06 21:36:36 $"
__copyright__ ... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/diveintopython-pdf-5.4/diveintopython-5.4/py/soundex/stage1/soundex1b.py | Python | mit | 2,305 | [
"VisIt"
] | 6df8a0d1ebdf1d594e09de11e24ecdb113ab24240eab6da60104b170ec848d17 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2014 Google 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 applicabl... | GoogleCloudPlatform/gce-oreilly | ch7-2.py | Python | apache-2.0 | 5,251 | [
"VisIt"
] | caa8e73a9c55a839d6ad3f4c99d1e4b2cf025587b5b82a38a77c221f16e3cbf4 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkTransformTextureCoords(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | chrisidefix/devide | modules/vtk_basic/vtkTransformTextureCoords.py | Python | bsd-3-clause | 503 | [
"VTK"
] | 27d1b3855b8b42c13632fcc50ad83cc6911060a93b020d758bf8d8a15f4b31a4 |
# Copyright 2014-2017 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... | blond-admin/BLonD | __EXAMPLES/mpi_main_files/EX_10_Fixed_frequency.py | Python | gpl-3.0 | 5,276 | [
"Gaussian"
] | 8c045c456377623189049432e17fd4907e74f1d1e52625629446d1241f1da078 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""Tests for the unique domains visited analysis plugin."""
import unittest
from plaso.analysis import unique_domains_visited
from plaso.engine import queue
from plaso.engine import single_process
from plaso.lib import timelib
from plaso.lib import event
from tests.analysis ... | ostree/plaso | tests/analysis/unique_domains_visited.py | Python | apache-2.0 | 2,969 | [
"VisIt"
] | 53e24fa0857172e51d19bfb9d227f001308035cf406903476b7936378ae879c8 |
"""This is the state that handles battles against
monsters"""
import random, sys, copy
from itertools import izip
import pygame as pg
from .. import tools, battlegui, observer, setup, entityclasses, compositeclasses, spellhandler, itemhandler
from .. components import person, attack, attackitems
from .. import constant... | 2Guys1Python/Project-Cacophonum | data/states/battle.py | Python | mit | 40,020 | [
"BLAST"
] | 8f5838df0fa070023803f26a39c9f30193fff8dcacbb1b6a20184e50a8418d37 |
import sys
import os
import json
import re
import io
import urllib
import requests
import logging
import time
from requests_toolbelt import MultipartEncoder
import subprocess
from zipfile import ZipFile
from os import listdir
from os.path import isfile, join
from biokbase.workspace.client import Workspace
def stderrl... | kbaseIncubator/core_genome_utilities | lib/biokbase/genome_util/script_util.py | Python | mit | 7,593 | [
"BLAST"
] | 4a40db82e29da47f978fc300a31d4c0dd7612537ea53a02cc389feba79c23ae3 |
########################################
#Globale Karte fuer tests
# from Rabea Amther
########################################
# http://gfesuite.noaa.gov/developer/netCDFPythonInterface.html
import math
import datetime as DT
from datetime import datetime
from matplotlib.dates import DayLocator, HourLocator, DateForm... | CopyChat/Plotting | Python/Mei_rsds_sst.py | Python | gpl-3.0 | 4,939 | [
"NetCDF"
] | c1569a564a532aefe70621f36e4c92e3aea85af144138bd4d1f49985add8894c |
############################################################################
##
## Copyright (C) 2006-2010 University of Utah. All rights reserved.
##
## This file is part of VisTrails.
##
## This file may be used under the terms of the GNU General Public
## License version 2.0 as published by the Free Software Foundat... | VisTrails/vistrails-contrib-legacy | vtksnl/base_module.py | Python | bsd-3-clause | 8,489 | [
"VTK"
] | 6bb0273e9aed3f88a3798cc87a0cebdb5e6ed47ca3092df609389886747d0c8f |
"""This module provides wrappers for vtkDataObjects.
The data objects does not have any sort of spatial reference.
"""
import numpy as np
from pyvista import _vtk
import pyvista
from pyvista.utilities import (FieldAssociation, assert_empty_kwargs, get_array,
row_array)
from .dataset im... | akaszynski/vtkInterface | pyvista/core/objects.py | Python | mit | 13,439 | [
"VTK"
] | 26bd5cfd02951bf725cff90171b79bc554797942729a25f5a455d32eefa642f9 |
##
# 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... | valtandor/easybuild-easyblocks | easybuild/easyblocks/n/netcdf_fortran.py | Python | gpl-2.0 | 2,782 | [
"NetCDF"
] | 368914c244b4afa30a6d6a166d2e423dd72336a940a80a5b75d803557fb6a432 |
#!/usr/bin/env python3
# Tool to discover 'smells' in the Discogs data dump. It prints a list of URLs
# of releases that need to be fixed.
#
# Why this happens:
#
# https://www.well.com/~doctorow/metacrap.htm
#
# Currently the following smells can be discovered:
#
# * depósito legal :: until recently the "depósito leg... | armijnhemel/cleanup-for-discogs | cleanup-discogs.py | Python | gpl-3.0 | 86,839 | [
"CASINO"
] | 9aba5158f2feef0b3bcb23d82696a4c846e0c39b16fc145380a4df6708b7be13 |
import os
from os.path import join as pjoin
from warnings import warn
import numpy as np
from scipy import stats, ndimage, misc
from matplotlib.colors import colorConverter
import nibabel as nib
from mayavi import mlab
from mayavi.tools.mlab_scene_model import MlabSceneModel
from mayavi.core.ui.api import SceneEdito... | aestrivex/PySurfer | surfer/viz.py | Python | bsd-3-clause | 96,471 | [
"Mayavi"
] | 6f56bdd9b4a057332084bd339893c93bd44f8f9555c89d70ef7d40975285bda4 |
import vtk
from vtk.util.colors import eggshell, slate_grey_light, red
from vtk.util import numpy_support
from vtk.numpy_interface import dataset_adapter as dsa
from vtk.numpy_interface import algorithms as alg
import mabdi
import numpy as np
import matplotlib.pyplot as plt
import time
import logging
logging.basi... | lucasplus/MABDI | scripts/TestFilterPointCloud.py | Python | bsd-3-clause | 2,255 | [
"VTK"
] | 180dfdcb0597cff36cf1c039b4a7239703c7f9f92653a34a44e298ce41fc782a |
#--------------------------------------------------------------------
from importing import \
finish_object, \
load, \
load_brick, \
load_callback, \
load_cgo, \
load_coords, \
load_embedded, \
load_map, \
... | gratefulfrog/lib | python/pymol/api.py | Python | gpl-2.0 | 11,451 | [
"PyMOL"
] | f4ec7115729dfdede60a8415b4c178e036333fe1df5b965c45dbdff8e4c82aea |
import os
import vtk, qt, ctk, slicer
import logging
from SegmentEditorEffects import *
import vtkITK
import SimpleITK as sitk
import sitkUtils
import math
class SegmentEditorEffect(SegmentEditorThresholdEffect):
""" LocalThresholdEffect is an effect that can perform a localized threshold when the user ctrl-clicks o... | lassoan/SlicerSegmentEditorExtraEffects | SegmentEditorLocalThreshold/SegmentEditorLocalThresholdLib/SegmentEditorEffect.py | Python | bsd-3-clause | 26,878 | [
"VTK"
] | 6d3b1c011c7b6b69929102e6986ea6e7324d36c398dbd97986591b19190f0bb4 |
r"""OS routines for NT or Posix depending on what system we're on.
This exports:
- all functions from posix, nt or ce, e.g. unlink, stat, etc.
- os.path is either posixpath or ntpath
- os.name is either 'posix', 'nt' or 'ce'.
- os.curdir is a string representing the current directory ('.' or ':')
- os.pardir... | bgris/ODL_bgris | lib/python3.5/os.py | Python | gpl-3.0 | 36,950 | [
"VisIt"
] | e5846cea70449fe842588de41bcc4e9fc3fde20a9d1d4f864ef02647799756ba |
#!/usr/bin/env python
import pandas
import netCDF4 as nc
import argparse
"""
Read a list of edits which were provided by and apply them to a topo file.
"""
parser = argparse.ArgumentParser()
parser.add_argument('--orig',type=str,help='path to original netCDF file',default=None)
parser.add_argument('--edits',type=str... | nicjhan/MOM6-examples | land_ice_ocean_LM3_SIS2/OM_360x320_C180/preprocessing/applyTopoEdits.py | Python | gpl-3.0 | 2,789 | [
"NetCDF"
] | 8e826ce2cad39a749cd11227288ea06a90d19c1e5056bd4ae2a7282a67d0a435 |
import functools
from ctypes import c_double
from ctypes import c_float
from ctypes import c_int
from ctypes import c_void_p
from ctypes import cast
from ctypes import POINTER
from ctypes import pointer
from ctypes import Structure
from enum import IntEnum
import numpy as np
from parcels.tools.converters import TimeC... | OceanPARCELS/parcels | parcels/grid.py | Python | mit | 27,628 | [
"NetCDF"
] | b30dbfa4f5a235d7d84176db39e4519e170512d1b9c4e3dfd454c78fabf78d37 |
import re
from copy import deepcopy
from warnings import warn
from ast import NodeTransformer, And
from six import iteritems, string_types
from ..core.Gene import eval_gpr, parse_gpr, ast2str
def prune_unused_metabolites(cobra_model):
"""Removes metabolites that aren't involved in any reactions in the model
... | pstjohn/cobrapy | cobra/manipulation/delete.py | Python | gpl-2.0 | 8,601 | [
"VisIt"
] | 740bd88d3c30e0f3a572bb955f3ea3ee636848f427deba14a930b956b459dc9e |
#!/usr/bin/env python
"""
@package run
Run a MD simulation in OpenMM. NumPy is required.
Copyright And License
@author Lee-Ping Wang <leeping@stanford.edu>
All code in this file is released under the GNU General Public License.
This program is free software: you can redistribute it and/or modify it under
the ter... | pandegroup/tip3p-tip4p-fb | OpenMM/OpenMM-MD.py | Python | mit | 68,599 | [
"Amber",
"Dalton",
"Gaussian",
"OpenMM",
"TINKER"
] | fedaa6d3bcd1ce28685332de4ffff1c4d80d0a5446dbea15beeaaf700719fdf1 |
"""
Multi course Discount coupons tests
"""
import random
from unittest import skip
from regression.pages.whitelabel.course_about_page import CourseAboutPage
from regression.tests.helpers.coupon import Coupon
from regression.tests.helpers.coupon_consts import (
BENEFIT_TYPE, BENEFIT_VALUE, CATALOG_QUERY, COUPON_T... | edx/edx-e2e-tests | regression/tests/whitelabel/test_dynamic_discount_coupon.py | Python | agpl-3.0 | 2,584 | [
"VisIt"
] | ee3147ad361ae112c33d2c30d9d3f555923c31173fcb2440fa5e76a096115de9 |
"""This module provides classes that allow Numpy-type access
to VTK datasets and arrays. This is best described with some examples.
To normalize a VTK array:
import vtk
import vtk.numpy_interface.dataset_adapter as dsa
import vtk.numpy_interface.algorithms as algs
rt = vtk.vtkRTAnalyticSource()
rt.Update()... | hlzz/dotfiles | graphics/VTK-7.0.0/Wrapping/Python/vtk/numpy_interface/dataset_adapter.py | Python | bsd-3-clause | 42,049 | [
"VTK"
] | b6f24722bafbada3fbc9da9388c9484654c5188b91be50e7690797003a529c17 |
import os
import numpy as np
from scipy.io import loadmat
# Set the random seed for reproducibility
seed = np.random.randint(2**16)
print "Seed: ", seed
np.random.seed(seed)
import matplotlib.pyplot as plt
from optofit.models.model import Model, DataSequence
from optofit.population.population import Population
from ... | HIPS/optofit | examples/fit_als_control_neuron.py | Python | gpl-2.0 | 6,902 | [
"NEURON"
] | 386a333228e484c2c61dfed55488c9a1cbed00e4ed3ebb8f3aae9dd22edd59eb |
import os
from datetime import datetime, timedelta
from hashlib import md5
from time import time
def __get_random_string(length=500):
"""
Return a random string
:param length: Length
:type length: inte
:rtype: str
"""
return md5(os.urandom(length)).hexdigest()
def _get_random_visitor_id... | KuwaitNET/django-shorter | tinylinks/piwik.py | Python | mit | 1,646 | [
"VisIt"
] | fef98223577a54bf19ff569d714ea69ce1a1ee33b73e0361d2ee257ccb3a9cb1 |
try:
from setuptools import setup
except:
from distutils.core import setup
import os
setup(
name = 'MIDAS',
version = '1.3.0',
description = 'An integrated pipeline and for estimating species and strain-level genomic variation from metagenomic data',
license = 'GPL',
author = 'Stephen Nayfach',
author_email='s... | snayfach/PhyloCNV | setup.py | Python | gpl-3.0 | 482 | [
"Biopython",
"pysam"
] | bd2238a74d90ab58d2cc37323248b4f764be67ba456fbc433e9c4f51d9a72f35 |
# 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 u... | szha/mxnet | python/mxnet/gluon/probability/block/stochastic_block.py | Python | apache-2.0 | 4,729 | [
"Gaussian"
] | 18a3323767d67025aa603a744daeb54c6ac569cc1ede3d11c4969ebdd724c24f |
"""
@package medpy.io.save
Provides functionality connected with image saving.
The supplied methods hide more complex usage of a number of third party modules.
@author Oskar Maier
@version r0.1.1
@since 2012-05-28
@status Release
"""
# build-in modules
import os
# third-party modules
import scipy
# own modules... | kleinfeld/medpy | medpy/io/save.py | Python | gpl-3.0 | 11,663 | [
"VTK"
] | 79c2f0972900e0b9e42aee64810a3f43efd544598b5a9dea77404111aff90b2b |
# Copyright (c) 2012-2014, Max Zwiessele, James Hensman
# Licensed under the BSD 3-clause license (see LICENSE.txt)
"""
Introduction
^^^^^^^^^^^^
Certain :py:class:`GPy.models` can be instanciated with an `inference_method`. This submodule contains objects that can be assigned to `inference_method`.
Inference over G... | SheffieldML/GPy | GPy/inference/latent_function_inference/__init__.py | Python | bsd-3-clause | 5,261 | [
"Gaussian"
] | 82e006afcdcf9713eb63987d5293159619fe48702aaa1f7a16e9f94c5ca302f1 |
"""
Created on Aug 7, 2016
@author: tjoneslo
"""
import os
import logging
import math
from Map import GraphicMap
from Galaxy import Galaxy
from AllyGen import AllyGen
from PyRoute.FontLayer import FontLayer
from PIL import Image, ImageDraw, ImageColor, ImageFont
class GraphicSubsectorMap(GraphicMap):
positions =... | makhidkarun/traveller_pyroute | PyRoute/SubsectorMap2.py | Python | mit | 22,497 | [
"Galaxy",
"VASP"
] | b10d6e2fb58229b42e0a0321cbe30ad2a24d178b3b518d7ac8328aa918176a47 |
# -*- coding: utf-8 -*-
"""
@author: Rick Berg, University of Washington, School of Oceanography
Monte Carlo Simulation for interface flux model
Must run interface_flux model before running this script
Fit is introducing structure that isn't in the data
"""
import numpy as np
from scipy import optimize, integrate, s... | rickdberg/mgmodel | interface_flux_montecarlo.py | Python | mit | 10,046 | [
"Gaussian"
] | 470ef49ab97cd3f1af281cbcc24181a5367d8708590ac299089f51beac4f186e |
from ase.structure import molecule
from gpaw import GPAW
from gpaw.odd.sic import SIC
from gpaw import extra_parameters
from gpaw.test import equal
extra_parameters['sic'] = True
n = molecule('N')
n.center(vacuum=3)
calc = GPAW(xc=SIC(nspins=2),
h=0.2,
convergence=dict(eigenvalues=1e-5, densit... | robwarm/gpaw-symm | gpaw/test/big/odd/n2.py | Python | gpl-3.0 | 671 | [
"ASE",
"GPAW"
] | 96a2bc866ee887704ec77b18c95e943421d940efa089370d1d811cb7431fb7cb |
import multiprocessing
import threading
import weakref
from typing import Any, MutableMapping, Optional
try:
from dask.utils import SerializableLock
except ImportError:
# no need to worry about serializing the lock
SerializableLock = threading.Lock
try:
from dask.distributed import Lock as Distributed... | shoyer/xarray | xarray/backends/locks.py | Python | apache-2.0 | 5,294 | [
"NetCDF"
] | f82e21fc2a82be17d68c0adb177bc51271d7c16a356dc3a500d2ca5cb18193b1 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
urlpatterns = [
url(r'^$', TemplateView.as_view(templ... | boweeb/nhweb | config/urls.py | Python | bsd-3-clause | 1,227 | [
"VisIt"
] | ab225b85cf8bc76f088736f485c62f052662aac41ffc9df7a9a61d75219117b2 |
import os, sys
from . import util
class Bwa:
def __init__(self,version="default", samtools_version="default"):
try:
self.bwa_cmd=util.programs["bwa"][version]
except KeyError, e:
print >>sys.stderr, "Cannot find specified version of bwa in configuration file: %s" % versio... | rhshah/cmo | cmo/bwa.py | Python | gpl-2.0 | 2,387 | [
"BWA"
] | b8086aff8d4103f84c40a59e1c3aec2e360bd971639d9280953a15581880dfd8 |
#/*
# *
# * OpenVPN for Kodi.
# *
# * Copyright (C) 2015 Brian Hornsby
# *
# * 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) any late... | xcafebabe/script.openvpn | resources/lib/kodisettings.py | Python | gpl-3.0 | 2,002 | [
"Brian"
] | 47f6f5abc6c46a42ab7b4fa84ad883e1e30575e231b7d6fbc2e8497fd3081541 |
# This test runs through the steps described in the python trace tutorial
# to appear in a Kitware Source newsletter.
#
# Trace is enabled and the following actions are captured and then replayed:
#
# An octree fractal source is created, dimension set to 3, contour filter is
# applied, then the active source is chan... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/ParaViewCore/ServerManager/Default/Testing/Python/PythonSMTraceTest1.py | Python | gpl-3.0 | 3,069 | [
"ParaView"
] | 5f64af5d63c8952d0125a49faa79f5737cab9e5690fc8257716a7250d481f973 |
import numpy as np
from tvtk.api import tvtk
from mayavi.scripts import mayavi2
@mayavi2.standalone
def main():
# Create some random points to view.
pd = tvtk.PolyData()
pd.points = np.random.random((1000, 3))
verts = np.arange(0, 1000, 1)
verts.shape = (1000, 1)
pd.verts = verts
pd.point_... | HPCGISLab/STDataViz | WorkingVersion/Scatter_plot.py | Python | bsd-3-clause | 932 | [
"Mayavi"
] | 5e4819dd9218ab0c60d191dcbb7e0f5fb522d1687da9becc15d17bd81a8f5127 |
"""Support for control of ElkM1 lighting (X10, UPB, etc)."""
from homeassistant.components.light import (
ATTR_BRIGHTNESS, SUPPORT_BRIGHTNESS, Light)
from . import DOMAIN as ELK_DOMAIN, ElkEntity, create_elk_entities
DEPENDENCIES = [ELK_DOMAIN]
async def async_setup_platform(
hass, config, async_add_ent... | jamespcole/home-assistant | homeassistant/components/elkm1/light.py | Python | apache-2.0 | 1,643 | [
"Elk"
] | 29a81cac624c968d3d9b2674dac29a9231fc5e82df965bb7ee1e33bba17fcf17 |
"""
=========================================
Robust line model estimation using RANSAC
=========================================
In this example we see how to robustly fit a line model to faulty data using
the RANSAC algorithm.
"""
import numpy as np
from matplotlib import pyplot as plt
from skimage.measure import ... | jwiggins/scikit-image | doc/examples/transform/plot_ransac.py | Python | bsd-3-clause | 1,589 | [
"Gaussian"
] | 85acfba3d105513ecb7e71afcfdb6c2ff6152a2e8894fba00eb831e94f5e073b |
"""Gets all residues contacting receptor in PDB.
To run this script, open ``pymol`` in the directory where the script is found.
Then at the ``pymol`` command line type::
run get_RBS.py
This script was written by Jesse Bloom, 2014."""
def main():
"""Main body of script."""
# input / output files
pdb... | jbloom/mapmuts | examples/WSN_HA_2014Analysis/get_RBS.py | Python | gpl-3.0 | 1,597 | [
"PyMOL"
] | 8be3438be6f1e83dda20a2ed52fd92308000336dafb6ddbf1db9e93ba3457a34 |
'''PipelinePeakCalling.py - Tasks associated with pipeline_peakcalling
======================================================================
One set of functions runs peak callers and uploads the called peaks
into the database. The functions follow the following naming convention:
runXXX()
run a certain peak ca... | CGATOxford/CGATPipelines | obsolete/PipelinePeakcalling.py | Python | mit | 92,370 | [
"pysam"
] | 81df0715699474960993006f1c79c371811f61119bb41d52db891db98b5c032b |
"""
End to end tests for LMS Login
"""
import os
from bok_choy.web_app_test import WebAppTest
from regression.pages.lms import LMS_BASE_URL, LMS_STAGE_BASE_URL
from regression.pages.lms.dashboard_lms import DashboardPageExtended
from regression.pages.lms.login_lms import LmsLogin
class LoginTest(WebAppTest):
"... | edx/edx-e2e-tests | regression/tests/lms/test_lms_login.py | Python | agpl-3.0 | 2,030 | [
"VisIt"
] | a0d324bd89827568f0d40f8b3f364f2e9f1aa3513ba33d481d1bd3bf436565bb |
"""
Useful support routines (for internal use).
These functions aren't really Zero Install specific; they're things we might
wish were in the standard library.
@since: 0.27
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _, logger
imp... | afb/0install | zeroinstall/support/__init__.py | Python | lgpl-2.1 | 3,615 | [
"VisIt"
] | e1d30a89072c33a006ac9f1b4c3fa724e59f918ad22c74727e2b839e8a9becc9 |
# copied from oasys-wofry/orangecontrib/wofry/util/wofry_util.py
# TODO: centralize in OASYS?
import numpy, decimal
from PyQt5.QtGui import QFont, QPalette, QColor
from PyQt5.QtWidgets import QWidget, QGridLayout, QLabel, QDialog, QVBoxLayout, QDialogButtonBox
from matplotlib.patches import FancyArrowPatch, ArrowStyl... | srio/Orange-XOPPY | orangecontrib/xoppy/widgets/gui/image_view_with_fwhm.py | Python | bsd-2-clause | 14,408 | [
"Gaussian"
] | ea5ab6c477e9be2102d2e5b3932672ac9b9fb383c6f48aaac7838764135a52ac |
"""
Objective:
Workflow steps overview:
1. Relax 2D and Bulk Competitors
2. Calculate Stability diagram
3. Prep a dummy IBZKPT
4. Run HSE band structure
5. Run +U calibrations
6. Run AFM calcualtions
7. Run Anisotropy calculations
"""
#### IMPORTS ####
##GENERAL python imports##
import os
import sys
from collection... | joshgabriel/MPInterfaces | mpinterfaces/workflows.py | Python | mit | 9,929 | [
"VASP",
"pymatgen"
] | 91e2fe45915b80220f6d8b6087effb106dcf1f206707b3ab933051843484040c |
########################################################################
# File : VirtualMachineDB.py
# Author : Ricardo Graciani
# occi and multi endpoint author : Victor Mendez
########################################################################
""" VirtualMachineDB class is a front-end to the virtual machines ... | DIRACGrid/VMDIRAC | VMDIRAC/WorkloadManagementSystem/DB/VirtualMachineDB.py | Python | gpl-3.0 | 52,165 | [
"DIRAC"
] | 23e23ccbcbcd5e56c951debd9220661f8dd77cbb5ded3a322b3a5d80789bb40b |
# -*- 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 'item.brand_name'
db.delete_column(u'salesReport_item', 'brand_name')
def backwards(s... | akiokio/centralfitestoque | src/salesReport/migrations/0033_auto__del_field_item_brand_name.py | Python | bsd-2-clause | 8,180 | [
"VMD"
] | 1adb4ddbeff3b9f314fc0a1a808de5fc2cf3c23bd053e5cc86e9ce2bc1326e09 |
from pypers.core.step import Step
import os
import re
class bowtie2(Step):
spec = {
"version": "2015.11.20",
"descr": [
"Run bowtie2 mapping for fastq reads, paired or unpaired"
],
"args":
{
"inputs": [
{
"name" ... | frankosan/pypers | pypers/steps/mapping/bowtie2.py | Python | gpl-3.0 | 6,829 | [
"Bowtie"
] | 8a30a5cc4230d435e5968e3a2a7848f1777b5c6cad4a2c708d5618bada1ac036 |
from __future__ import print_function, division
from sympy.core import sympify, Lambda, Dummy, Integer, Rational, oo, Float, pi
from sympy.core.compatibility import xrange
from sympy.functions import sqrt, exp, erf
from sympy.printing import sstr
from sympy.utilities import default_sort_key
import random
class Samp... | ojengwa/sympy | sympy/statistics/distributions.py | Python | bsd-3-clause | 14,927 | [
"Gaussian"
] | 663fe4d6ec5e2668dddc79ee773a3ed060eebb5ddc956af0b8b86bcc4e8de9f6 |
# Copyright: (c) 2019, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import (absolute_import, division, print_function)
__metaclass__ = type
import errno
import fnmatch
import json
import operator
import os
import shutil
import stat
import... | 2ndQuadrant/ansible | lib/ansible/galaxy/collection.py | Python | gpl-3.0 | 46,035 | [
"Galaxy"
] | b472baaae8ea2814604e3165a8e3fd59efdc49864a35e267e80d69096de52039 |
from django.template.loader import render_to_string
from django.utils.translation import ugettext_lazy as _
from pressgang.actions.lockdown.exceptions import LockdownError
from pressgang.actions.lockdown.steps import LockdownStep
from pressgang.actions.options.utils import sitewide_activate_plugin
from pressgang.core... | oberlin/pressgang | pressgang/actions/lockdown/steps/caching.py | Python | bsd-3-clause | 11,370 | [
"VisIt"
] | bf5b6c87c0fa030efc31b9cde702ac376d6358e2d3b935cde9092dd498ba0e0c |
from __future__ import absolute_import
from .Errors import error, message
from . import ExprNodes
from . import Nodes
from . import Builtin
from . import PyrexTypes
from .. import Utils
from .PyrexTypes import py_object_type, unspecified_type
from .Visitor import CythonTransform, EnvTransform
try:
reduce
except N... | ryfeus/lambda-packs | HDF4_H5_NETCDF/source2.7/Cython/Compiler/TypeInference.py | Python | mit | 22,326 | [
"VisIt"
] | b3e18a65cab5e8a3cf818fcea45f1c4e54265f50a9bbea81302b660180e0f1f7 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Jan 2018
do metropolis sampling to estimate PDF of chessboard calibration. this involves
intrinsic and extrinsic parameters, so it's a very high dimensional search
space (before it was only intrinsic)
@author: sebalander
"""
# %%
#import glob
import os
im... | sebalander/sebaPhD | dev/intrinsicCalibFull.py | Python | bsd-3-clause | 16,067 | [
"Gaussian"
] | bacaf024e494e0cbc5680783906a0b9ae36145b3a9271d2976c8640010260e8e |
#!/usr/bin/env python
"""annotate a BSR matrix,
based on a GenBank file"""
from __future__ import print_function
import optparse
import sys
import os
from Bio import SeqIO
import subprocess
from collections import OrderedDict
from operator import itemgetter
def test_file(option, opt_str, value, parser):
try:
... | jasonsahl/LS-BSR | tools/annotate_matrix_by_locus_tags.py | Python | gpl-3.0 | 7,024 | [
"BLAST"
] | 438dfc74cd7abcf2849582f5811abfc493c12a1ba57f399db35c62b6801305c3 |
## begin license ##
#
# "Meresco Solr" is a set of components and tools
# to integrate Solr into "Meresco."
#
# Copyright (C) 2011-2013 Seecr (Seek You Too B.V.) http://seecr.nl
# Copyright (C) 2012 SURF http://www.surf.nl
# Copyright (C) 2013 Stichting Bibliotheek.nl (BNL) http://www.bibliotheek.nl
# Copyright (C) 20... | seecr/meresco-solr | meresco/solr/cql2solrlucenequery.py | Python | gpl-2.0 | 2,057 | [
"VisIt"
] | fd00cfb7837440521fa7a8c9fe9e9d6d77e2c329948fbf065035c41673ad719f |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
Symmetry is not immutable
CASSCF solver can have different symmetry to reference Hartree-Fock calculation.
'''
import pyscf
mol = pyscf.M(
atom = 'Cr 0 0 0',
basis = 'cc-pvtz',
spin = 6,
symmetry = True,
)
myhf = mol.RHF(... | sunqm/pyscf | examples/mcscf/20-change_symmetry.py | Python | apache-2.0 | 1,051 | [
"PySCF"
] | 8c1984a1753ef0c68387e7890c0ec87af2135506f2842eb6cc0b9221bd8a4f71 |
# coding=utf-8
# Copyright 2018 The Tensor2Tensor 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... | rsepassi/tensor2tensor | tensor2tensor/layers/modalities.py | Python | apache-2.0 | 19,549 | [
"Gaussian"
] | 3078fcfa7b549a5cf5caf342dc3cbf49a74ae6f17bf6a2124235987c380deeeb |
""" Correlated gaussian random variables.
Objects of type :class:`gvar.GVar` represent gaussian random variables,
which are specified by a mean and standard deviation. They are created
using :func:`gvar.gvar`: for example, ::
>>> x = gvar.gvar(0, 0.3) # 0 +- 0.3
>>> y = gvar.gvar(2, 0.4) # 2... | gplepage/gvar | src/gvar/__init__.py | Python | gpl-3.0 | 51,003 | [
"Gaussian"
] | b97eb0c0ede3cfe703b5443a28e686105a4c0a20b5e78f20882db62102557227 |
import numpy as np
from ase.units import Bohr
from ase.lattice import bulk
from gpaw import GPAW, FermiDirac
from gpaw.response.df import DielectricFunction
from gpaw.test import equal, findpeak
a = 6.75 * Bohr
atoms = bulk('C', 'diamond', a=a)
calc = GPAW(mode='pw',
kpts=(3, 3, 3),
eigensolve... | robwarm/gpaw-symm | gpaw/test/diamond_absorption.py | Python | gpl-3.0 | 2,007 | [
"ASE",
"GPAW"
] | 1f8df03ee33d774d20a0e88232c4544305f3c79c4de373b9e929e5c6a266447f |
#Implementation by Brian Beck from
# http://code.activestate.com/recipes/410692/
class switch(object):
def __init__(self, value):
self.value = value
self.fall = False
def __iter__(self):
"""Return the match method once, then stop"""
yield self.match
raise StopIteration... | mac389/brainpy | lib/switch.py | Python | gpl-3.0 | 627 | [
"Brian"
] | 9feb0d39fe96b80ccb2e7d188510ead1bf78f37d9e73a07782aa8c0210780bdf |
""" Encapsulate here the logic for matching jobs
Utilities and classes here are used by MatcherHandler
"""
__RCSID__ = "$Id"
import time
from types import StringTypes
from DIRAC import gLogger, gMonitor
from DIRAC.Core.Utilities.ClassAd.ClassAdLight import ClassAd
from DIRAC.Core.Security import Properties
fro... | marcelovilaca/DIRAC | WorkloadManagementSystem/Client/Matcher.py | Python | gpl-3.0 | 13,715 | [
"DIRAC"
] | a4cce1deee3b67075f6839d36f86bd15012ef4247746a8fd8f6f64fed95b6846 |
"""
@name: PyHouse/Project/src/_test/testing_mixin.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2013-2020 by D. Brian Kimmel
@license: MIT License
@note: Created on Jun 4, 2013
@summary: Test handling the information for a house.
"""
from Modules.Core.Config import C... | DBrianKimmel/PyHouse | Project/src/_test/testing_mixin.py | Python | mit | 3,611 | [
"Brian"
] | aa322d7bbceb0da42272de5a000fbe4fe482521cc37e5a692548f9ac3a9c6fb4 |
#!/usr/bin/env python
import os,sys
import re
import time
import fastq
import fileinput
import multiprocessing
from PIL import Image, ImageDraw
from multiprocessing import Process, Queue
from bubbledetector import BubbleDetector
########################### BubbleProcesser
class BubbleProcesser:
__polyR... | haploxer/deBubble | bubbleprocesser.py | Python | mit | 14,824 | [
"pysam"
] | da81fda64a4a68a5a4a76152fcbdf3090b595bd0012083e64d63ef056ae17137 |
#
#
#Custom filename tags to distinguish from other runs
project = "SunEarth"
runVers = "Test"
#Project specific notes:
# Test case:
# Star: Sun
# Spectrum: Na I D region
# Lightcurve: Earth, in plane of ecliptic
#Default plot
#Select ONE only if plotting 'inline' -
makePlotStruc = True
makeP... | sevenian3/ChromaStarPy | Input.py | Python | mit | 4,025 | [
"Gaussian"
] | dca24318c81f82346b7ef492dfb425f06bc21c2a85beceb89690d6aebfb20331 |
# -*- coding: utf-8 -*-
"""QGIS Unit tests for edit widgets.
.. note:: 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.
"""
__au... | uclaros/QGIS | tests/src/python/test_qgsrelationeditwidget.py | Python | gpl-2.0 | 17,770 | [
"Galaxy"
] | 4526d96bb1c9262281d35ea31deff9cf8d1d606fadf35948dc2ae31284c2a6f4 |
"""
MtGoxHMAC v0.01
Copyright 2011 Brian Monkaba
This file is part of ga-bitbot.
ga-bitbot 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) an... | Pascal66/ga-bitbot | MtGoxHMAC.py | Python | gpl-3.0 | 11,262 | [
"Brian"
] | 962f927b30f50c63486b21536faaf9758d9886e4d8b8e981cec2cff406721b0b |
# -*- coding: utf-8 -*-
"""
Example script to set up the parameters for the image processing pipeline
"""
######################### Import modules
import os, numpy, math
import ClearMap.Settings as settings
import ClearMap.IO as io
from ClearMap.Alignment.Resampling import resampleData;
from ClearMap.Alignment.Elas... | ChristophKirst/ClearMapUnstable | ClearMap/Scripts/parameter_file_template.py | Python | gpl-3.0 | 10,467 | [
"Gaussian",
"VTK"
] | 9b2fab874dce370aab38d0d36d3623719b6f7458a2027480111dd7b40052187b |
# Reorganizes pipeline directory structure from before 8/14/2015
import os
import glob
import argparse
parser = argparse.ArgumentParser()
parser.add_argument('--prefix', default='*')
args = parser.parse_args()
if args.prefix=='*':
# Find qsub_command
import os, inspect
dirs = {}
dirs['script'] = os.path.dirn... | luizcieslak/AlGDock | Pipeline/reorganize_pipeline.py | Python | mit | 6,310 | [
"NetCDF"
] | 795046f232bd2adf266d686fb8e30b3c18e3f0cfcc9102a30fcbb33946f57511 |
from loguru import logger
import sys
import os
import os.path as op
# from collections import namedtuple
# from scipy.io import loadmat, savemat
import scipy
import scipy.ndimage
import numpy as np
import imma.image_manipulation as ima
def segmentation_replacement(
segmentation,
segmentation_new,
... | mjirik/lisa | lisa/segmentation_general.py | Python | bsd-3-clause | 3,489 | [
"Gaussian"
] | 7fd731c477fa1857d059b9834d881007db437731577c80e2708889ef6a9d276f |
#!/usr/bin/python
#FILE DESCRIPTION=======================================================
#~ Python script used for post-processing automatization of the rivulet
#~ flow down the experimental plate in Freiberg
#~
#~ NOTES:
#~ - creates a scalar clip for deltaf >= 1e-5
#~ - adds case description
#~ - adds ... | MartinIsoz/CFD_oF | 05_freibergExpSetUp/00_Scripts/rivuletPostProc_rPFF.py | Python | gpl-2.0 | 6,975 | [
"ParaView"
] | 4a83c84e0bdebdf7949e23b4b8ee44ad4f1f331255c1ef5f32b66875b10e8746 |
# -*- coding: utf-8 -*-
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | vidartf/hyperspy | hyperspy/model.py | Python | gpl-3.0 | 70,365 | [
"Gaussian"
] | 6df1c9b447ef4f5070e75159ccf21ec20bfed36fdbd444aa9591e4d6c0053feb |
import json
import os
from os.path import join, expanduser
from optparse import OptionValueError
from GangaDirac.Lib.Utilities.DiracUtilities import write_env_cache
import GangaCore.Utility.Config
from GangaCore.Utility.execute import execute
from GangaCore.Utility.logging import getLogger
from GangaCore.Core.exceptio... | ganga-devs/ganga | ganga/GangaLHCb/Utility/LHCbDIRACenv.py | Python | gpl-3.0 | 2,271 | [
"DIRAC"
] | af2852c68d350ed16598f9ba597f581c674a71f38097ce82a2b04396cd1ae7d2 |
# Copyright 2002, 2003 Ben Escoto
#
# This file is part of rdiff-backup.
#
# rdiff-backup is free software; you can redistribute it and/or modify
# 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.
... | makinacorpus/rdiff-backup | rdiff_backup/FilenameMapping.py | Python | gpl-2.0 | 9,147 | [
"VisIt"
] | d07bba5a25e19783d9b24762dba310d82b51f90bcc979ad0e00325340087dd91 |
# 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 u... | sxjscience/tvm | python/tvm/relay/testing/py_converter.py | Python | apache-2.0 | 26,109 | [
"VisIt"
] | 6aec8cb7b53b54178af7cd7ef78cdf68a7f2c88c20820339af8472d8b2419fa4 |
"""
Python interface to GnuPG.
This module is used to invoke GnuPG to check the digital signatures on interfaces.
@see: L{iface_cache.PendingFeed}
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _, logger
import subprocess
import base... | timdiels/0install | zeroinstall/injector/gpg.py | Python | lgpl-2.1 | 10,663 | [
"VisIt"
] | 715d6fbb9eeb9e5b7cb20447657ff5499498ae9550bb8da3e8c81bc66aa1bc9b |
# -*- coding: utf-8 -*-
#
# pymatgen documentation build configuration file, created by
# sphinx-quickstart on Tue Nov 15 00:13:52 2011.
#
# This file is execfile()d with the current directory set to its containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# Al... | gmatteo/monty | docs_rst/conf.py | Python | mit | 9,363 | [
"pymatgen"
] | c5423195e09dd36d38d7faf7d559e1099f7906307c958dc33e22d47270f96758 |
"""Functions to plot M/EEG data on topo (one axes per channel)
"""
from __future__ import print_function
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eri... | antiface/mne-python | mne/viz/topo.py | Python | bsd-3-clause | 20,339 | [
"Gaussian"
] | 5f67b3d38034517e8a7f08f6604ba7a80b2f37448a2f463fc468361c2ebf073a |
# -*- coding: utf-8 -*-
{
"'Cancel' will indicate an asset log entry did not occur": "'Abbrechen' wird angeben, dass ein Asset Log Eintrag nicht eingetreten ist",
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that... | gallifrey17/eden | languages/de.py | Python | mit | 255,398 | [
"VisIt"
] | 78bc22b888854a08c6c544e32f380193af5c52b8719b1c22a5a4a00d0c354283 |
from unittest import TestCase
import unittest
import pygem.utils as ut
import pygem.params as pars
import numpy as np
import filecmp
import os
import vtk
class TestUtils(TestCase):
def test_utils_write_original_box(self):
params = pars.FFDParameters()
params.read_parameters(filename='tests/test_datasets/para... | fsalmoir/PyGeM | tests/test_utils.py | Python | mit | 1,975 | [
"VTK"
] | 76e29c7496268af97844c924f8107e2910446491a2a3a0a0642c653436983ad5 |
#! /usr/bin/env python3
"""
Usage:
python3 Main.py <filename>
python3 Main.py --three-addr <filename>
"""
from MuLexer import MuLexer
from MuParser import MuParser
from MyMuCodeGen3AVisitor import MyMuCodeGen3AVisitor
from Allocations import alloc_to_mem, alloc_naive
from ExpandJump import replace_jump
import ... | lauregonnord/cap-labs | TP05/Mu-codegen/Main.py | Python | gpl-3.0 | 2,479 | [
"VisIt"
] | 284e5ec8c5602b83e6aaf4b9e8e571f18daa588bdc0519c5f6dc882d5827a545 |
#!/usr/bin/env python
"""Detector that can be used to experiment with different carrier peak
interpolation methods.
Example usage:
python -m "thrifty.experimental.detect_carrier_interpol" \
--method cosine rx.card -o rx.data
"""
from __future__ import print_function
import argparse
from thrifty.detec... | swkrueger/Thrifty | thrifty/experimental/detect_carrier_interpol.py | Python | gpl-3.0 | 2,242 | [
"Gaussian"
] | 972cbedcd02c35b1d7740487a72c666df32072c6ad15496606ab26bad3d51809 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/web/zap.py | Python | gpl-2.0 | 5,174 | [
"VisIt"
] | 0640e97bd7569a68e7032636d4fc68cb186e7c9850bc8d4e8e28f3d31f8b8ed6 |
# Copyright 2019 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... | renyi533/tensorflow | tensorflow/python/keras/layers/preprocessing/image_preprocessing.py | Python | apache-2.0 | 43,743 | [
"Gaussian"
] | 257baf8b72e069351315bb220cc3cfaed0889207ce1264cd14e5642b6a99fb41 |
"""This demo program demonstrates how to mark sub domains of a mesh
and store the sub domain markers as a mesh function to a DOLFIN XML
file.
The sub domain markers produced by this demo program are the ones used
for the Stokes demo programs.
"""
# Copyright (C) 2007 Kristian B. Oelgaard
#
# This file is part of DOLF... | MiroK/DolfinSurface | demo/undocumented/subdomains/python/demo_subdomains.py | Python | gpl-3.0 | 2,815 | [
"VTK"
] | 5c20183a005bf217b055531e55a0553de0bf923f1308a229ab8fb9e1ae281ad3 |
#!/usr/bin/env python
# This example demonstrates the use of vtkLabeledDataMapper. This
# class is used for displaying numerical data from an underlying data
# set. In the case of this example, the underlying data are the point
# and cell ids.
import vtk
# Create a selection window. We will display the point and ... | naucoin/VTKSlicerWidgets | Examples/Annotation/Python/labeledMesh.py | Python | bsd-3-clause | 4,426 | [
"VTK"
] | 7b859e441fdded3508bced3696891c0b1a10a0b4c4b1e408f28a4085b959f3cd |
import numpy as np
from numpy.testing import (
assert_,
assert_array_almost_equal,
)
from MDAnalysisTests.datafiles import MMTF, MMTF_gz
from MDAnalysis.coordinates.MMTF import MMTFReader
class TestMMTFReader(object):
def setUp(self):
self.r = MMTFReader(MMTF)
def tearDown(self):
de... | alejob/mdanalysis | testsuite/MDAnalysisTests/coordinates/test_mmtf.py | Python | gpl-2.0 | 1,867 | [
"MDAnalysis"
] | d6dde2dca3bf41c16aba054e3d55fec4ec2b3e7146b446a947cb4e4b58d2a40a |
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