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# This file is part of sydpy.
#
# Copyright (C) 2014-2015 Bogdan Vukobratovic
#
# sydpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 2.1
# of the License, or (at your option)... | bogdanvuk/sydpy | sydpy/_util/_util.py | Python | lgpl-2.1 | 5,818 | [
"VisIt"
] | fa9ac03cf0c7085fc0bf89e945c80f90992773500e51e79538a0cca41c9c9fcf |
import global_vars
import os
import exceptions
import smtplib
import email.mime.text
class Task_exception(exceptions.Exception):
def __init__(self,message):
self.message=message
def __str__(self):
return " Task error:"+message
class Task:
def __init__(self,db_row):
self.user_id = db_row[0]
... | Abi1ity/uniclust2.0 | old_uniclust_model/task.py | Python | bsd-3-clause | 7,430 | [
"VisIt"
] | 14f7e845f9dbf6f838da85899a85dcb9468a3e330cdef917fffe7d5123c2d1ef |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# king_phisher/server/server_rpc.py
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice... | 0x0mar/king-phisher | king_phisher/server/server_rpc.py | Python | bsd-3-clause | 14,731 | [
"VisIt"
] | 59047019088de3091b90df1d38f04343e683d624388830c48a12bd2e46907ce7 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2008 Jerome Rapinat
# Copyright (C) 2008 Benny Malengier
# Copyright (C) 2010 Gary Burton - derived from _HasGalleryBase.py
#
# This program is free software; you can redistribute it and/or modify
# it under t... | beernarrd/gramps | gramps/gen/filters/rules/source/_hasrepository.py | Python | gpl-2.0 | 2,659 | [
"Brian"
] | f1aa777f675651741b2c4f65052e88764582a0e66ac1befa9f5740269ec622e5 |
from __future__ import division, print_function, absolute_import
import warnings
import numpy as np
from dipy.reconst.odf import OdfModel, OdfFit
from dipy.reconst.cache import Cache
from dipy.reconst.multi_voxel import multi_voxel_model
from dipy.reconst.shm import (sph_harm_ind_list,
rea... | maurozucchelli/dipy | dipy/reconst/csdeconv.py | Python | bsd-3-clause | 23,359 | [
"DIRAC"
] | 1f935d280851c5d24905fbf0f8d166635ff8bc6ca3aa2f7cc0aa12e2637e210b |
from ase import Atoms
from gpaw import GPAW
a = 2.87
bulk = Atoms('Fe2',
positions=[(0, 0, 0),
(a/2, a/2, a/2)],
cell=(a, a, a),
pbc=True)
calc = GPAW(kpts=(6, 6, 6),
h=0.20,
nbands=18,
eigensolver='cg',
txt... | qsnake/gpaw | doc/exercises/iron/non.py | Python | gpl-3.0 | 415 | [
"ASE",
"GPAW"
] | e574f42435c03c9bbe9fe65392d6713647ffface5c56f3e9a598d53e695bcb06 |
'''TB Animation Tools is a toolset for animators
*******************************************************************************
License and Copyright
Copyright 2015-Tom Bailey
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public Licen... | tb-animator/tbtools | apps/tb_isolator.py | Python | mit | 1,668 | [
"VisIt"
] | 8c10af6f30543fec7be8adb4df3b08e91c9888f51fb61701d23c2e178412e8ff |
##
# Copyright (C) 2012 Jasper Snoek, Hugo Larochelle and Ryan P. Adams
#
# This code is written for research and educational purposes only to
# supplement the paper entitled
# "Practical Bayesian Optimization of Machine Learning Algorithms"
# by Snoek, Larochelle and Adams
# Advances in Neural Information Processing... | claesenm/optunity-benchmark | optimizers/spearmint/spearmint_april2013_mod_src/GPEIOptChooser.py | Python | gpl-3.0 | 25,968 | [
"Gaussian"
] | ab8d33527597a4c8e52bb85803340d4b100e500ddf3f74133ac5cb0db699982a |
# -*- coding: utf-8 -*-
"""
Created on Fri Mar 20 12:55:12 2015
This file is (slightly modified) from Fabrizio Costa's EDeN.
Copyright 2015 Nicolo' Navarin
This file is part of scikit-learn-graph.
scikit-learn-graph is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public ... | nickgentoo/scikit-learn-graph | skgraph/datasets/obabel.py | Python | gpl-3.0 | 2,446 | [
"Pybel"
] | 5a935fc6b7ba4e1cdbc3e1ff5d7b3b0d93c6f7e866031fdfcb4d966eabb2c47b |
import sys
import traceback
import optparse
import numpy as np
from ase.structure import bulk, estimate_lattice_constant
from ase.atoms import Atoms, string2symbols
from ase.data.molecules import molecule
from ase.visualize import view
from ase.io import read, write
from ase.constraints import FixAtoms
from gpaw.util... | qsnake/gpaw | gpaw/utilities/gpawscript.py | Python | gpl-3.0 | 7,953 | [
"ASE",
"CRYSTAL",
"GPAW"
] | f86c0b03d88a44ad70c191e534aae21ba11755e3ae08b7bc2a3086ac93f55cf0 |
import operator
from glob import glob
import os
import re
import warnings
import numpy as np
import dask.array as da
import xray
from xray import Variable
from xray.backends.common import AbstractDataStore
from xray.core.utils import NDArrayMixin
from xray.core.pycompat import OrderedDict
from xray.core.indexing impo... | rabernat/xgcm-examples | _xgcm/mdsxray.py | Python | mit | 23,927 | [
"NetCDF"
] | 16568499d99c520923baa813f4ade448f9b940ada39ebfdf36e55d8e0e7e82de |
#!/usr/bin/env python
# ----------------------------------------------------------------------------
# Copyright 2015-2016 Nervana Systems 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
#... | Jokeren/neon | tests/serialization/alexnet.py | Python | apache-2.0 | 4,215 | [
"Gaussian"
] | d02d8cc435f7efbf44db1818a79fa2aba200fc511e6e4d8f9d243c9ed2e0a7ce |
import logging
import operator
import os
from galaxy import util
from galaxy.util.bunch import Bunch
from galaxy.util.hash_util import new_secure_hash
from galaxy.model.item_attrs import Dictifiable
import tool_shed.repository_types.util as rt_util
from galaxy import eggs
eggs.require( 'mercurial' )
from mercurial imp... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/tool_shed/model/__init__.py | Python | gpl-3.0 | 18,249 | [
"Galaxy"
] | c034bb0a3385f4d531b3cf245f6948f2ca5a8a97de2967000b06ddbb9ea49d38 |
# coding=utf-8
from nose.tools import eq_
from csxj.datasources.parser_tools.utils import extract_plaintext_urls_from_text
class TestPlainTextURLExtractor(object):
def setUp(self):
self.simple_url = 'http://www.foo.com'
# fuck yeah gehol
self.complex_url = 'http://164.15.72.157:8080/Repor... | sevas/csxj-crawler | tests/datasources/parser_tools/test_url_extraction.py | Python | mit | 4,465 | [
"VisIt"
] | 91b721690b91a98b8d8922bc4f96b08da5fb4c67ccf4b9118d409a9da32dd15e |
"""Header value parser implementing various email-related RFC parsing rules.
The parsing methods defined in this module implement various email related
parsing rules. Principal among them is RFC 5322, which is the followon
to RFC 2822 and primarily a clarification of the former. It also implements
RFC 2047 encoded w... | Reflexe/doc_to_pdf | Windows/program/python-core-3.5.0/lib/email/_header_value_parser.py | Python | mpl-2.0 | 105,084 | [
"CRYSTAL"
] | 51bd6cc3b9da39376e2c93dd196ec92d2ecc961ce855826f9077965f480cbcce |
text_addresses = {'Altar': (0x180300, 256),
'Triforce': (0x180400, 256),
'Uncle': (0x180500, 256),
'Ganon1': (0x180600, 256),
'Ganon2': (0x180700, 256),
'Blind': (0x180800, 256),
'TavernMan': (0x180C00, 256),
... | LLCoolDave/ALttPEntranceRandomizer | Text.py | Python | mit | 10,990 | [
"VisIt"
] | 00d4543058a3a4c79a53f9dd167293860b9a268bc67d1ff611b5f5972acb92e0 |
#!/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... | harterj/moose | modules/geochemistry/test/tests/time_dependent_reactions/cooling.py | Python | lgpl-2.1 | 1,931 | [
"MOOSE"
] | 612ee009bc3610e227da448a3987562ebcd9a6d5b23e0b462301036b82e8fda7 |
#!/usr/bin/env python
"""
version 0.1
Minor version changes:
- pep8 can make output directories directly
Given a nucleotide sequence, get pfam stuff with their rest api, return
USAGE:
$ python snagnblast.py accessions.txt_or_accessions.csv /BLAST/directory/ /output/directory/
"""
print("Warning! This script is de... | nickp60/open_utils | grabHits/grabHits.py | Python | mit | 8,667 | [
"BLAST"
] | 82c72ec5035d0f9ef981ac154b50ab2037ecd229f1ce443dd0ff99d1d09d7ffb |
"""rbf - Radial basis functions for interpolation/smoothing scattered N-D data.
Written by John Travers <jtravs@gmail.com>, February 2007
Based closely on Matlab code by Alex Chirokov
Additional, large, improvements by Robert Hetland
Some additional alterations by Travis Oliphant
Interpolation with multi-dimensional t... | jamestwebber/scipy | scipy/interpolate/rbf.py | Python | bsd-3-clause | 11,970 | [
"Gaussian"
] | f1c4e0d52fb2b9c59cd778d183ea37b89c05ccaa7dbb3efd4a84883a16d41f4a |
"""Simple VTK scene.
This script displays a simple 3D scene containing a single actor (a
cube) that the user can interact with via the mouse and keyboard. The
purpose of the script is to illustrate the VTK visualization pipeline
and how to use VTK in Python.
You can run the script from the command line by typing
pyth... | RDeckers/ScientificVisualization-1TD389 | Assignments/getting_started/cube.py | Python | gpl-3.0 | 1,267 | [
"VTK"
] | 3738b3895350d3d146bc7c3c3a1d82371994cf8f162d3da902c0b1d618045973 |
#!/bin/env python
# Automatically translated python version of
# OpenSceneGraph example program "osgpointsprite"
# !!! This program will need manual tuning before it will work. !!!
import sys
from osgpypp import osg
from osgpypp import osgDB
from osgpypp import osgViewer
# Translated from file 'osgpointsprite.cpp... | JaneliaSciComp/osgpyplusplus | examples/rough_translated1/osgpointsprite.py | Python | bsd-3-clause | 3,976 | [
"Galaxy"
] | 2e9a6ef25545951a7d610c0557dfe0202d67cac52d49b53af096bedb46549d66 |
from __future__ import print_function
import sys
import numpy as np
from ase import Atoms
from ase.io import write, read
from ase.calculators.singlepoint import SinglePointCalculator
a = 5.0
d = 1.9
c = a / 2
atoms = Atoms('AuH',
positions=[(c, c, 0), (c, c, d)],
cell=(a, a, 2 * d),
... | suttond/MODOI | ase/test/fio/oi.py | Python | lgpl-3.0 | 3,087 | [
"ASE"
] | f2fd3f74cff265de65731cc374e4a6647ee2a7ddf86c138ef281bf53b1c1657e |
import logging
import os
from django.views.generic import View
from django.http import HttpResponse
from django.conf import settings
from django.utils.decorators import method_decorator
from django.views.decorators.csrf import ensure_csrf_cookie
class FrontendAppView(View):
"""
Serves the compiled frontend e... | Hawk94/dust | backend/views.py | Python | mit | 1,140 | [
"VisIt"
] | 0b52732016196c5c75b116f651d4ac9807a644a60e3fd2e008d8fab02ebbc355 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | googleapis/python-datalabeling | scripts/fixup_datalabeling_v1beta1_keywords.py | Python | apache-2.0 | 8,221 | [
"VisIt"
] | 6f1ed4daaacf9626f2685b017f174f0aba766601cacc473bc01e353459ccd356 |
__author__ = 'Thomas Rueckstiess, ruecksti@in.tum.de'
from scipy import random
from scipy.ndimage import minimum_position
from scipy import mgrid, zeros, tile, array, floor, sum
from pybrain.structure.modules.module import Module
class KohonenMap(Module):
""" Implements a Self-Organizing Map (SOM), also known a... | pybrain/pybrain | pybrain/structure/modules/kohonen.py | Python | bsd-3-clause | 3,079 | [
"NEURON"
] | 7261efcc126518bff5a96d7235783f96ed0390136078a2e24fc4b08760646d2c |
import numpy as np
import os
try:
import netCDF4 as netCDF
except:
import netCDF3 as netCDF
import matplotlib.pyplot as plt
import time
from datetime import datetime
from matplotlib.dates import date2num, num2date
import pyroms
import pyroms_toolbox
import _remapping
class nctime(object):
pass
def remap_bdry... | kshedstrom/pyroms | examples/Arctic_HYCOM/remap_bdry.py | Python | bsd-3-clause | 8,604 | [
"NetCDF"
] | 1a827caea52f98ba30fcacd1ccb08f73f3503e2cb9dcdd91fb1941e56c9e430d |
#!/usr/bin/env python
#
# Copyright (c) 2010-2011 Appcelerator, Inc. All Rights Reserved.
# Licensed under the Apache Public License (version 2)
#
# parse out Titanium API documentation templates into a
# format that can be used by other documentation generators
# such as PDF, etc.
import os, sys, traceback
import re... | arnaudsj/titanium_mobile | apidoc/docgen.py | Python | apache-2.0 | 15,559 | [
"VisIt"
] | 5a725c1d3b5eb0a84f6b566e612e6ad7f928b0875234c431874a851a46915a8e |
import unittest
from neural_network_with_connections import *
from unittest import TestCase
class NeuralNetworkTests(TestCase):
def test_connection_adds_to_incoming_and_outgoing_arrays(self):
neuron = Neuron(input=0)
neuron_2 = Neuron()
neuron.connect_child(neuron_2, weight=1)
#... | dev-coop/neural-net-hacking-examples | python/Part 1/neural_network_with_connections_tests.py | Python | mit | 1,233 | [
"NEURON"
] | 552c6109c5f1aebca60949cf2f837ee1f90241a4e0e925789ecbab5cbd9a3bfc |
#!/usr/bin/env python
""" Submission of test jobs for use by Jenkins
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
# pylint: disable=wrong-import-position,unused-wildcard-import,wildcard-import
import os.path
from DIRAC.Core.Base.Script import parseC... | ic-hep/DIRAC | tests/Jenkins/dirac-test-job.py | Python | gpl-3.0 | 1,896 | [
"DIRAC"
] | d5752d8aa6f74654aea3aa2ee8b6caadb2463dc9698673a6384c28cdf74a0142 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
All SI units
## Plot the firing rate vs current injection curve for a Cerebellar Granule Cell neuron
## Author: Aditya Gilra
## Creation Date: 2012-07-12
## Modification Date: 2012-07-12
Wednesday 15 July 2015 09:46:36 AM IST
Added... | dilawar/moose-full | moose-core/tests/python/neuroml/FvsI_CA1.py | Python | gpl-2.0 | 1,878 | [
"MOOSE",
"NEURON"
] | 8b7e48685cc2232c59ad07311f8de7a0f00d500cb610845dbf20af3064e0999b |
#!/usr/bin/env python
#===============================================================================
# Copyright 2015 Geoscience Australia
#
# 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
#... | ama-jharrison/agdc | agdc/agdc/abstract_ingester/mosaic_contents.py | Python | apache-2.0 | 9,888 | [
"NetCDF"
] | d2d0e63725e759a913d3bed63827e516a6de1d406fc19165314f48f0d75371d9 |
import numpy as np
from ase.lattice import bulk
from gpaw import GPAW
from gpaw.response.df import DielectricFunction
# Part 1: Ground state calculation
atoms = bulk('Al', 'fcc', a=4.043) # Generate fcc crystal structure for aluminum
calc = GPAW(mode='pw', # GPAW calculator initialization
... | robwarm/gpaw-symm | doc/tutorials/dielectric_response/aluminum_EELS.py | Python | gpl-3.0 | 849 | [
"ASE",
"CRYSTAL",
"GPAW"
] | 6b8437936a7db1aaf3e0d7fe87087c794dc57fcd49c8b784bd86ccb6bce8f25a |
"""
# Majic
# Copyright (C) 2014 CEH
#
# 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 pr... | NERC-CEH/jules-jasmin | job_runner/job_runner/post_processing_scripts/convert_fractional_file_for_visualisation.py | Python | gpl-2.0 | 4,837 | [
"NetCDF"
] | 35d1af4d318bc1efdba8721db86383598200f79e59bcb43a791e214226f3bc3f |
#!/usr/bin/env python
##
## @file test.py
## @brief AutoRunner for Python test scripts
## @author Akiya Jouraku
##
##<!---------------------------------------------------------------------------
## This file is part of libSBML. Please visit http://sbml.org for more
## information about SBML, and the latest versi... | mgaldzic/antimony | src/bindings/python/test.py | Python | bsd-3-clause | 2,786 | [
"VisIt"
] | 88dc1c104c0d9c7939413fc525970a2f73a97ff296a9dd5e4493f9039cf628ea |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/pbc/scf/test/test_stability.py | Python | apache-2.0 | 3,701 | [
"PySCF"
] | 8e396df7b39d9540065320525c858296ee33f3bf8fbacbbde4ba21ba33253f1c |
# -*- coding: UTF-8 -*-
import threading
from django.conf import settings
from django.db import models
from geonode.maps.owslib_csw import CatalogueServiceWeb
from geoserver.catalog import Catalog
from geonode.core.models import PermissionLevelMixin
from geonode.core.models import AUTHENTICATED_USERS, ANONYMOUS_USERS, ... | mbertrand/cga-worldmap | geonode/maps/models.py | Python | gpl-3.0 | 88,413 | [
"BWA",
"VisIt"
] | d944b0a38b685078234438d8d48640133e75fc8acc1551e9803f207025c9112d |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
import sys
from math import pi, sqrt
import numpy as np
from numpy.linalg import solve, inv
from ase.data import atomic_names
from gpaw.setup_data import SetupData
from gpaw.atom.configurations import configurations
from g... | robwarm/gpaw-symm | gpaw/atom/generator.py | Python | gpl-3.0 | 36,950 | [
"ASE",
"GPAW",
"Gaussian"
] | d97c06ebe0adb66fe426134d5d982db562053b28512640daf3bb36d65509da4f |
"""
Dashboard view and supporting methods
"""
import datetime
import logging
from collections import defaultdict
from completion.exceptions import UnavailableCompletionData
from completion.utilities import get_key_to_last_completed_course_block
from django.conf import settings
from django.contrib import messages
from... | philanthropy-u/edx-platform | common/djangoapps/student/views/dashboard.py | Python | agpl-3.0 | 37,548 | [
"VisIt"
] | 8c1347b0aef76b9c9bb31c29e4cb54a521f2f66d5401a6db7e545c0eca232be5 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/p4util/optproc.py | Python | gpl-2.0 | 4,749 | [
"Psi4"
] | b10879e0ac0b5419ff74c2231988086359a4a97f16457baed7127f051ed3fbdd |
#! /usr/bin/env python
import numpy as np
import ase.io
import ase
import os
import sys
sys.path.insert(0, '.')
import shutil
import quippy
from quippy.clusters import (HYBRID_ACTIVE_MARK, HYBRID_NO_MARK, HYBRID_BUFFER_MARK,
create_hybrid_weights,
... | marcocaccin/crack2Dglass | make_cluster_from_crack.py | Python | gpl-2.0 | 8,992 | [
"ASE"
] | a112fc780b3f1c01afc6cd58c36ca34ce6cc30d0dd616c6fac6d0cfd2bb75fa0 |
# -*- coding: utf-8 -*-
"""
Automatically generate Brian's reference documentation.
Based on sphinx-apidoc, published under a BSD license: http://sphinx-doc.org/
"""
import inspect
import sys
import os
from os import path
from .examplefinder import auto_find_examples
INITPY = '__init__.py'
OPTIONS = [... | brian-team/brian2cuda | brian2cuda/sphinxext/generate_reference.py | Python | gpl-2.0 | 9,655 | [
"Brian"
] | b3f2ac4490a8010374a0303f34b6c75668b6d35952c321cd1404889786763fd4 |
# Clustalw modules
"""
A set of classes to interact with the multiple alignment command
line program clustalw.
Clustalw is the command line version of the graphical Clustalx
aligment program.
This requires clustalw available from:
ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/.
functions:
o parse_file
o do_alignment... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/Clustalw/__init__.py | Python | apache-2.0 | 22,263 | [
"Biopython"
] | 411ad27ed22c484a03672a9ee4d70b16d5b6125c77c94b8c788f0efe3f9ec061 |
# Copyright (c) 2012 OpenStack Foundation
# 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 ... | angdraug/nova | nova/tests/compute/test_resource_tracker.py | Python | apache-2.0 | 61,231 | [
"exciting"
] | 5b00ed313e1b81ed450dbe4236f0821dec8b2acbc05a3375a005cef56b2ce684 |
"""
Provide a generic structure to support window functions,
similar to how we have a Groupby object.
"""
from __future__ import division
from collections import defaultdict
from datetime import timedelta
from textwrap import dedent
import warnings
import numpy as np
import pandas._libs.window as libwindow
import pa... | GuessWhoSamFoo/pandas | pandas/core/window.py | Python | bsd-3-clause | 83,431 | [
"Gaussian"
] | 8ed11ecbe3fab1aa2d1fed1e6dccc6304bb59f752206f642e0318f066d0f34d8 |
#!/usr/bin/env python
import sys
import unittest
import vtk
from PyQt5 import QtWidgets
from peacock.ExodusViewer.ExodusViewer import main
from peacock.utils import Testing
class TestExodusViewer(Testing.PeacockImageTestCase):
"""
Testing for ExodusViewer.
TODO: There is a rendering artifact that shows ... | backmari/moose | python/peacock/tests/exodus_tab/test_ExodusViewer.py | Python | lgpl-2.1 | 3,210 | [
"VTK"
] | 63cd65934bcceee85bb21eca20cceee52afd1cb17c2e808ddf478ed3dcb3dd6a |
##############################################################################
# adaptiveMD: A Python Framework to Run Adaptive Molecular Dynamics (MD)
# Simulations on HPC Resources
# Copyright 2017 FU Berlin and the Authors
#
# Authors: Jan-Hendrik Prinz
# Contributors:
#
# `adaptiveMD` is free software: ... | jrossyra/adaptivemd | adaptivemd/engine/openmm/openmm.py | Python | lgpl-2.1 | 10,478 | [
"MDTraj",
"OpenMM"
] | 60f0051a9cb75f9d3a522703eb0a079a43c664aabd8fe6f85447148878a2823c |
import re
import pytest
from .. import factories as f
pytestmark = pytest.mark.django_db
def test_signup_flow(base_url, browser, outbox):
f.create_usertype(slug='tutor', display_name='tutor')
# Sign-Up option should be present there
browser.visit(base_url)
sign_up_link = browser.find_by_text('Sign ... | shankisg/wye | tests/functional/test_user_flow.py | Python | mit | 2,457 | [
"VisIt"
] | 37a4fef3d7b811659691e2672e6410d1923ccfe4b200e7e65c6509fd0971d3de |
#
# Copyright (c) 2015 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | lach76/scancode-toolkit | src/scancode/utils.py | Python | apache-2.0 | 8,899 | [
"VisIt"
] | 93b8e92ce0f8f5bda670677eb89ef4df8db426d6343f26602ef4bda0104c57a2 |
from math import pi, cos, sin, sqrt, acos
from ase.atoms import Atoms
from ase.parallel import paropen
def read_xyz(fileobj, index=-1):
if isinstance(fileobj, str):
fileobj = open(fileobj)
lines = fileobj.readlines()
L1 = lines[0].split()
if len(L1) == 1:
del lines[:2]
natoms... | freephys/python_ase | ase/io/xyz.py | Python | gpl-3.0 | 1,225 | [
"ASE"
] | ccc23eddeb4bbc317b486f6f82cccbd3eeda2b94b529b8c7e16c71bf924790d3 |
""" Author: Hongyang Cheng <chyalexcheng@gmail>
Test #1: 2D Membrane-wrapped granular material
"""
from esys.escript import *
from esys.weipa import saveVTK
from esys.finley import ReadGmsh
from esys.escript.pdetools import Projector
from esys.escript.linearPDEs import LinearPDE,SolverOptions
from msFEM2DExplicit ... | chyalexcheng/multiscale | msTest1_explicit.py | Python | gpl-3.0 | 6,147 | [
"VTK"
] | 18f2611a46dfbc92f740f0a634212c5a24010a10aeccc4e27d646cbc042d2644 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2017 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB ... | yashdsaraf/scancode-toolkit | tests/cluecode/test_copyrights_ics.py | Python | apache-2.0 | 812,853 | [
"BLAST",
"Brian",
"VisIt"
] | 34d3dc6dadde31b30d000791faa91e7847a687599d524299ba157e9bf45e3cb0 |
# Copyright 2015-2019 Cedric RICARD
#
# This file is part of CloudMailing.
#
# CloudMailing is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any lat... | ricard33/cloud-mailing | deployment/fab/fabfile.py | Python | agpl-3.0 | 12,937 | [
"GULP"
] | ad87f34a91abed148d79c5f8836a52ad0d280f19ca6396c173bea6d2c0b58800 |
#!/usr/bin/env python
import vtk
from vtk.util.misc import vtkGetDataRoot
# create planes
# Create the RenderWindow, Renderer
#
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer( ren )
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# create pipeline
#
pl3d = vtk.vtkPLOT3... | naucoin/VTKSlicerWidgets | Graphics/Testing/Python/streamSurface2.py | Python | bsd-3-clause | 2,074 | [
"VTK"
] | 4adde1d41fcc6a285ac1bc690071d2b2346e5459a2dbecc498ef969b5efaeac0 |
#!/usr/bin/env python
import os
import sys
import time
import platform
import argparse
from datetime import datetime
from space_checker_utils import wget_wrapper
import ConfigParser
def create_directory(directory):
"""Create parent directories as necessary.
:param directory: (~str) Path of directory to be ... | DePierre/owtf | install/install.py | Python | bsd-3-clause | 10,142 | [
"VisIt"
] | 2d02eaaa92666fc776e64807508f8789c0236bb9bf6251e8d0a7b62cde62ef8f |
# !usr/bin/env python
# -*- coding: utf-8 -*-
#
# Licensed under a 3-clause BSD license.
#
# @Author: Brian Cherinka
# @Date: 2017-08-04 15:36:16
# @Last modified by: Brian Cherinka
# @Last Modified time: 2017-08-04 16:02:22
from __future__ import print_function, division, absolute_import
from sciserver import aut... | havok2063/SciScript-Python | python/sciserver/integrationtest.py | Python | apache-2.0 | 596 | [
"Brian"
] | 6986b8123d176e8f62a7c91f137ba100310f53975fbc59c2538dc88eb8f35384 |
from setuptools import setup, find_packages
import re
VERSIONFILE = "pymaid/__init__.py"
verstrline = open(VERSIONFILE, "rt").read()
VSRE = r"^__version__ = ['\"]([^'\"]*)['\"]"
mo = re.search(VSRE, verstrline, re.M)
if mo:
verstr = mo.group(1)
else:
raise RuntimeError("Unable to find version string in %s." %... | schlegelp/pymaid | setup.py | Python | gpl-3.0 | 1,845 | [
"NEURON"
] | 698ae89b5e6d52536b902fddb9bdf69d13947acc398b028b6afaa915772c9088 |
#
# Copyright 2020 Johannes Hoermann (U. Freiburg)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# 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 F... | libAtoms/matscipy | matscipy/electrochemistry/utility.py | Python | lgpl-2.1 | 1,955 | [
"Matscipy"
] | 4fb9e74cca79b302c327c56a65f550ade6850795e3228e9e40456851f6643073 |
#!/usr/bin/env python
import os, sys, numpy as np, cPickle as pickle, copy
import sim, pickleTraj, parse_potential as pp
# user input
NB = None
NW = None
AATraj = None
Prefix = None
FF_File = None
# System conditions
TempSet = 300
Name_W = 'W' ; Name_B = 'B'
Mass_W = 18.01 ; Mass_B = 78.11
# Pair potential settings... | tanmoy7989/benwat | ti.py | Python | gpl-2.0 | 11,514 | [
"Gromacs",
"LAMMPS"
] | 2c2c182afcc6ae2724125a853e21bad9d366bda14e7da99e757b77d7cda5281e |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at https://mozilla.org/MPL/2.0/.
from pathlib import Path
import pytest
import os.path as osp
from sisl import geom
from sisl import Geometry, Atom
from ... | zerothi/sisl | sisl/io/siesta/tests/test_fdf.py | Python | mpl-2.0 | 15,227 | [
"SIESTA"
] | eb70974b781b0e153f52083b814769df693bbc30741bc320070197a796976a04 |
from django.db import models
from edc_base.audit_trail import AuditTrail
from edc_base.model.models import BaseUuidModel
from edc_constants.choices import ARV_STATUS_WITH_NEVER
from edc_constants.choices import YES_NO
from edc_constants.constants import NOT_APPLICABLE
from edc_sync.models import SyncModelMixin
from ed... | botswana-harvard/microbiome | microbiome/apps/mb_maternal/models/maternal_arv_post.py | Python | gpl-2.0 | 4,064 | [
"VisIt"
] | 213edcbc400d51edac2724fa4d4b589d16e6e52fe9f9eeb64c8b2e506cd0c115 |
from __future__ import absolute_import
import re
import json
import time
import logging
import random
import six
from django.conf import settings
from django.core.cache import cache
from six.moves.urllib.parse import parse_qsl
from sentry import http
from sentry.utils.strings import count_sprintf_parameters
logger... | alexm92/sentry | src/sentry/lang/javascript/errormapping.py | Python | bsd-3-clause | 3,763 | [
"VisIt"
] | c5adc601d03d7ff7fafcdfaf5de401eab9e1d95f8f2eb468022ae1c6a3845cdf |
#!/usr/bin/env python
#
# threat_note v3.0 #
# Developed By: Brian Warehime #
# Defense Point Security (defpoint.com) #
# October 26, 2015 #
#
import argparse
import csv
import hashlib
import io
import r... | defpoint/threat_note | threat_note/threat_note.py | Python | apache-2.0 | 42,723 | [
"Brian"
] | f93118cbfc3f325a39adbfa88517ba55cdf223c6c3bbffd8950c6236f2722214 |
import os, sys, getopt
try:
from PyQt4 import QtCore, QtGui
QtCore.Signal = QtCore.pyqtSignal
QtCore.Slot = QtCore.pyqtSlot
except ImportError:
try:
from PySide import QtCore, QtGui
QtCore.QString = str
except ImportError:
raise ImportError("Cannot load either PyQt or PySide... | katyhuff/moose | gui/vtk/ExodusResultRenderWidget.py | Python | lgpl-2.1 | 50,695 | [
"VTK"
] | a37c17114577108c0b4832cc0d407613b4ebe6545c3d81948f7bfe9cf2ecf23b |
# Copyright (C) 2002 Greg Landrum and Rational Discovery LLC
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2 of the License, or (at your option) any later version.
... | ptosco/rdkit | rdkit/sping/Qt/pidQt.py | Python | bsd-3-clause | 11,286 | [
"RDKit"
] | bca7440dcca96da5a2b75024a25b2ee71e906eccf6af62759364a4ba29563521 |
import os
import numpy as np
import time
import desispec
import astropy.io.fits as fits
from astropy.table import Table
from astropy.convolution import convolve, Box1DKernel
import json
import glob
import yaml
from pkg_resources import resource_filename
from scipy.optimize import minimize
from scipy.interpolate impo... | desihub/desispec | py/desispec/tsnr.py | Python | bsd-3-clause | 48,790 | [
"Galaxy",
"Gaussian"
] | 40201fe37be48faf4a829d9a06269e62bd747f1dd374b0b505f942119d9760a0 |
#!/usr/bin/python
__author__ = ('David Dunn')
__version__ = '0.1'
import cv2, os, math, sys
import numpy as np
# All measurements are in meters
#pixelDiameter = .000042333 # .0042333cm = 1/600 in (600dpi)
#pixelDiameter = .000333333333 # (3 dpmm)
#pixelDiameter = .0001 # (10 dpmm)
def strToImg(text, scale=1.0,th... | qenops/dGraph | util/imageManip.py | Python | apache-2.0 | 12,240 | [
"Gaussian"
] | 70dd7e50bbad7a20a6f79dd88cbb824a942ef6e790b2790464e308e55a646f23 |
# -*- coding: utf-8 -*-
import skimage.io
import skimage.feature
import skimage.color
import skimage.transform
import skimage.util
import skimage.segmentation
import numpy
# "Selective Search for Object Recognition" by J.R.R. Uijlings et al.
#
# - Modified version with LBP extractor for texture vectorization
def _... | tpsatish95/OCR-on-Indus-Seals | code/Test/selectivesearch.py | Python | apache-2.0 | 8,799 | [
"Gaussian"
] | 8a4afc71082768de48a7b5e2afbe1295f87e391e56eee67744d7d65d50842eab |
#!/usr/bin/env python
import vtk
import numpy as np
from vmtk import vmtkscripts
import argparse
import copy
# creates lines normal to surface for evaluation in the probe image with surface
def warp_surface(args):
print("get lines along normal of surface")
reader = vmtkscripts.vmtkSurfaceReader()
re... | kayarre/Tools | vmtk/warpsurface.py | Python | bsd-2-clause | 3,846 | [
"VTK"
] | 9b1e8744a014261ca9659d931f2e1caf4799782a1ca41ed308099453a8fcd66b |
"""
Acceptance tests for studio related to the outline page.
"""
import json
from datetime import datetime, timedelta
import itertools
from pytz import UTC
from bok_choy.promise import EmptyPromise
from nose.plugins.attrib import attr
from ...pages.studio.settings_advanced import AdvancedSettingsPage
from ...pages.stu... | solashirai/edx-platform | common/test/acceptance/tests/studio/test_studio_outline.py | Python | agpl-3.0 | 81,678 | [
"VisIt"
] | 51f610717c9c07630bc5b4d402c378e65336e33554f3ab5287844bf2accf71f4 |
"""
The ``fatiando`` package contains all the subpackages and modules required for
most tasks.
Modules for each geophysical method are group in subpackages:
* :mod:`gravmag <fatiando.gravmag>`:
Gravity and magnetics (i.e., potential fields)
* :mod:`seismic <fatiando.seismic>`:
Seismics and seismology
* :mod:`geot... | seancug/python-example | fatiando-0.2/fatiando/__init__.py | Python | gpl-2.0 | 2,087 | [
"Mayavi"
] | b7ec935d188be614b8be75d49cb804e4822b3d5d5b58fc9d72c2620b255dc11d |
"""
Tests for geography support in PostGIS 1.5+
"""
import os
from django.contrib.gis import gdal
from django.contrib.gis.measure import D
from django.test import TestCase
from models import City, County, Zipcode
class GeographyTest(TestCase):
def test01_fixture_load(self):
"Ensure geography features load... | nycholas/ask-undrgz | src/ask-undrgz/django/contrib/gis/tests/geogapp/tests.py | Python | bsd-3-clause | 3,472 | [
"VisIt"
] | 60c4716f9018953455c6d6fe602af59679cde32ca94ca8c9bc4e09ad84a9b81b |
import click
import os
def get_host(host):
"""
Based on the host agrumement passed in, determine which host to pass back.
"""
# WIP: Only aws for now!
from skipper.aws.host import host
return host
class BaseHost(object):
def check_file(self, message):
exists = False
while... | cameronmaske/skipper | skipper/hosts.py | Python | bsd-2-clause | 1,632 | [
"VisIt"
] | e9900d4d51ce44bb5a8c6dbf47b0f5b3a06ff7c45a15a171c46c8870677b8fd7 |
"""
Module to set up run time parameters for Clawpack.
The values set in the function setrun are then written out to data files
that will be read in by the Fortran code.
"""
import os
import numpy as np
#------------------------------
def setrun(claw_pkg='amrclaw'):
#------------------------------
""... | torrilhon/MyClawpack | examples/stokes_2d_drivencavity/setrun.py | Python | gpl-3.0 | 11,383 | [
"NetCDF"
] | 20f79b1e456b46b4e15b0d1e2c7ce92a54645fcb1453d4e21e8e336bede1e61c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# This file is part of the PyNeurActiv project, which aims at providing tools
# to study and model the activity of neuronal cultures.
# Copyright (C) 2017 SENeC Initiative
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of th... | SENeC-Initiative/PyNeurActiv | analysis/bayesian_blocks.py | Python | gpl-3.0 | 13,573 | [
"Gaussian"
] | 67d70e8aa8e7485a86dece8e03fd6790b1afdcb489d84a7dd48b1470bb75619a |
import math
import numpy as np
__all__ = ["plot_disks_1d", "plot_disks"]
def plot_disks_1d(plt, pts, weights, total_area):
"""Plot a circles at quadrature points according to weights. The diameters
sum up to the total area.
"""
radii = 0.5 * abs(weights) / math.fsum(weights) * total_area
colors ... | nschloe/quadpy | src/quadpy/helpers/plot.py | Python | mit | 8,907 | [
"Mayavi",
"VTK"
] | 3817a6aa42f46108402137960fc86185cf9a4367c3a309a3b9637e3c77ee5735 |
"""
Test rdkit_grid_featurizer module.
"""
import os
import unittest
import numpy as np
np.random.seed(123)
from deepchem.feat import rdkit_grid_featurizer as rgf
def random_string(length, chars=None):
import string
if chars is None:
chars = list(string.ascii_letters + string.ascii_letters + '()[]+-.=#@/\\')... | ktaneishi/deepchem | deepchem/feat/tests/test_rdkit_grid_features.py | Python | mit | 23,883 | [
"RDKit"
] | a5dac4af989526c372177aef735f2d91c5c8d51e4fb5b7fc2bf2df2c29e79265 |
''' Volume processing for next round of refinement.
This pySPIDER batch file (`spi-prepvol`) takes sets of three volumes (full volume and two half volumes)
produced by alignment/refinement and then does the following:
#. Masks the half volumes
#. Calculates the resolution between the half volumes
... | ezralanglois/arachnid | arachnid/pyspider/prepare_volume.py | Python | gpl-2.0 | 14,002 | [
"Gaussian"
] | 7e8a5aba845cc697fdedaddf1140bf20ae09a3916b35d8b32d2b38ea52936ce8 |
import copy
import itertools
import megadb.tree as tree
import megadb.algebra as algebra
from megadb.algebra.parser import print_parse_tree
class BaseOptimizator(object):
def run(self, tree):
raise NotImplementedError()
def tree_traverse(root, type, visit):
children = root.children[:] if isinstance(... | itswindtw/pyMega | megadb/optimization/optimizator.py | Python | mit | 31,843 | [
"VisIt"
] | 8d7cf604d6e99c73e1c70be8aeeef703dcdcb315ce9e75309347c9e5e00270bd |
#
# Copyright (c) 2016 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | tests/scancode/test_api.py | Python | apache-2.0 | 2,534 | [
"VisIt"
] | ca20e486c32430ae298936779aa769954a458be6082808fb4468a013aadf28cc |
#!/usr/bin/env python2
"""Script to retrieve and back up calendars and contacts from Google."""
import datetime
import httplib2
import os
import sys
from apiclient import discovery
from gdata import gauth
from gdata.contacts import client as contacts_client
from oauth2client import client as oauth_client
from oauth2c... | toastwaffle/GData-Backup | backup.py | Python | mit | 7,896 | [
"VisIt"
] | 5664a374fa8487afa348a210af57bd525b06a4d01f475f211b6312706fccc946 |
# -*- coding: utf-8 -*-
#
"""Testing script for wlsqm, doubles as a usage example.
-JJ 2016-11-10
"""
from __future__ import division, print_function, absolute_import
import time
import numpy as np
import sympy as sy
import scipy.spatial # cKDTree
import matplotlib.pyplot as plt
import mpl_toolkits.mplot3d.axes3... | Technologicat/python-wlsqm | examples/wlsqm_example.py | Python | bsd-2-clause | 52,676 | [
"Gaussian"
] | 491ec84afcbef3646c8084d37fbbe961cf28b732990516af0a5a935d15625c2f |
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.gov.br
# License: ... | givanaldo/invesalius3 | invesalius/data/polydata_utils.py | Python | gpl-2.0 | 6,513 | [
"VTK"
] | 027ac74bafd16d9ebe6da314a6aec2833cbecf9a74c466a78aead89c2613490c |
# Copyright 2014-2020 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 required by appl... | sunqm/pyscf | pyscf/pbc/df/test/test_mdf_ao2mo.py | Python | apache-2.0 | 4,910 | [
"PySCF"
] | 59906813e3be4cb9a6153d369816de555b6b0466a264693a455e0cafd38898f2 |
#!/usr/bin/python
# -*- coding: UTF-8 -*-
# Introduction: This script used to get G+C content
# 3rd position of synonymous codons (GC3s)
# from each fasta format sequence
# Input is a Seq format object (Bio.SeqIO)
# Created by galaxy on 17-3-12 4:12pm
def read_seq(seq):
s... | cvn001/codonPY | src/get_GC3s_from_fasta.py | Python | mit | 926 | [
"Galaxy"
] | ecb35480746c5037f5c1013d5873c565c34b9ef8faecab0a8fd9d43c34295ba6 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
########### Attension
# [n] means n-dimension array
# [m x n] means (m x n)-dimension array
# no [] means 1-dimension data
import random as rand
import numpy as np
import numpy.linalg as nplnlg
import neuro_function as nf
class NeuroElement:
def __init__(self) : ... | WaterIsland/DLStudy | mln/BatchLearning/Mln.py | Python | mit | 17,689 | [
"NEURON"
] | eed8b300c43b1b9677b343bdc4b7f9e40637d2c97b30d1d4052153bc190e8dd7 |
try:
import freenect
except:
print "No freenect support"
import logging
import numpy as np
from threading import Thread
import time
MAXDEPTH = 1200
FRAMEBYTES = 640*480*2
class KinectLoop(Thread):
def __init__(self, server, **kwargs):
super(KinectLoop, self).__init__(**kwargs)
self.serv... | parthaa/Kimotion | server/input.py | Python | gpl-2.0 | 4,836 | [
"Gaussian"
] | 5e128e6a0bfea110ec30ad2b2ae5ff4cb0a843e8e2b785f02b66d350174c6dd2 |
#
# python-ipfix (c) 2013 Brian Trammell.
#
# Many thanks to the mPlane consortium (http://www.ict-mplane.eu) for
# its material support of this effort.
#
# This program is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the Free
# Softw... | britram/python-ipfix | ipfix/ieutils.py | Python | lgpl-3.0 | 2,386 | [
"Brian"
] | 53e2f4eb5a57865d11444d847fb1e0062142c690d88b25f3e428cfe6ae860fd2 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RRbgl(RPackage):
"""An interface to the BOOST graph library
A fairly extensive and... | LLNL/spack | var/spack/repos/builtin/packages/r-rbgl/package.py | Python | lgpl-2.1 | 1,084 | [
"Bioconductor"
] | f24660b58fa3160a7cca110765f3cdc1f716d1a801969aff69c3ad507b86986c |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import socket
import time
import os
try:
import selectors
except ImportError:
import selectors2 as selectors
from DIRAC.Core.DISET.private.Transports.BaseTransport import BaseTrans... | ic-hep/DIRAC | src/DIRAC/Core/DISET/private/Transports/PlainTransport.py | Python | gpl-3.0 | 4,874 | [
"DIRAC"
] | ec14b14655e5cbc0b167e37389a76dc5c508578bc02ab9fd923fef0ef5fcfd5d |
"""
Calculated formation energies for inorganic crystals from Materials Project.
"""
import os
import deepchem as dc
from deepchem.molnet.load_function.molnet_loader import TransformerGenerator, _MolnetLoader
from deepchem.data import Dataset
from typing import List, Optional, Tuple, Union
MPFORME_URL = 'https://deepc... | deepchem/deepchem | deepchem/molnet/load_function/material_datasets/load_mp_formation_energy.py | Python | mit | 4,318 | [
"CRYSTAL"
] | 3ac43596436f4a7898ea485eac86d8123a09dce877404eb6c7285aa599f54315 |
#!/usr/bin/python
# Copyright 2007-2011 David Michael Bryson, all rights reserved.
# http://programerror.com/software/testrunner
#
# Redistribution and use in source and binary forms, with or without modification, are permitted provided that the
# following conditions are met:
#
# 1. Redistributions of source... | rholder613/AvidaAR | avida-master/avida-core/tests/_testrunner/testrunner.py | Python | gpl-2.0 | 41,438 | [
"Brian"
] | 32df6344f17362c2819cb85fab82561b2494d334288649605d0257d77d1bacc7 |
# Shared methods for the github email hook and cron job
#
# Copyright (C) 2015 Red Hat, Inc.
#
# This copyrighted material is made available to anyone wishing to use,
# modify, copy, or redistribute it subject to the terms and conditions of
# the GNU General Public License v.2, or (at your option) any later version.
# ... | rhinstaller/github-email-hook | github_email_hook/__init__.py | Python | gpl-2.0 | 6,225 | [
"VisIt"
] | b6e927b107ad45eadf307b597a3b360c9d503a3116bc35a2fa3befab44a8c1bc |
#!/usr/bin/python
import os
import task
import sys
import pipeline
#import QC
#import Bwa
lib_path = os.path.abspath(os.path.join('drmaa-python'))
sys.path.append(lib_path)
import drmaa
p = pipeline.pipeline();
p.clean()
p.processApp()
p.pj_initialize()
p.run()
#print "Log> Job Start"
#q = TT.TT()
#q.setName("TT task... | s4553711/HiScript | src/main.py | Python | mit | 361 | [
"BWA"
] | d3ea8e7aedab531b173f09a569eb85aa9d62304519e3ecee42408ba4970179bd |
from ...utils.helpers import CacheDict
from ...exceptions import SmtlibError
from .expression import *
from functools import lru_cache
import copy
import logging
import operator
import math
import threading
from decimal import Decimal
logger = logging.getLogger(__name__)
class Visitor:
"""Class/Type Visitor
... | trailofbits/manticore | manticore/core/smtlib/visitors.py | Python | agpl-3.0 | 38,537 | [
"VisIt"
] | a3543cf1c448b3ab4b5fbeacdb31eef924cd668269d1db214bdb38a024d1455a |
#
# ui: user interface module for graphical handling
# Copyright (C) 2012 cmiN
#
# 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 lat... | cmin764/xhosts | xhosts/ui.py | Python | gpl-3.0 | 8,005 | [
"VisIt"
] | 87d9391bb9d267bc84693584cbde37a78baf4b9018cac7a91b1b89531994d5aa |
"""
pyaircraft.io.read_p3_flight
=========================
This is a grouping of scripts designed to process NOAA P-3
flight level data recorded during flights and put into NetCDF
format by NOAA AOC.
Created by Nick Guy.
"""
# NOTES:: This has only been tested with DYNAMO data files, versions
# may change... | nguy/pyparticleprobe | pyparticleprobe/io/read_p3_flight.py | Python | lgpl-2.1 | 4,960 | [
"NetCDF"
] | cc8056a53246a646f51eaec9e488249e0c3f8cec29487da369b951a5ec49d643 |
#!/usr/bin/env python
import numpy
import itertools
from pymatgen.core.lattice import Lattice
from pymatgen.core.operations import SymmOp
from pymatgen.core.structure import Structure
from crystal import fillcell, tikz_atoms
def trilayer(doped = None):
a = 5.43
fcc = Lattice([[a/2,a/2,0],[a/2,0,a/2],[0,a/2,a... | ldamewood/figures | scripts/trilayer.py | Python | mit | 1,564 | [
"CRYSTAL",
"pymatgen"
] | c7e84fe12f1511e8f4e0febf14f1fcbec13fcd6252e2760edf987881eb2d52e3 |
#!/usr/bin/env python3
"""
Template by pypi-mobans
"""
import os
import sys
import codecs
import locale
import platform
from shutil import rmtree
from setuptools import Command, setup, find_packages
# Work around mbcs bug in distutils.
# http://bugs.python.org/issue10945
# This work around is only if a project sup... | chfw/pyexcel-ods | setup.py | Python | bsd-3-clause | 5,214 | [
"VisIt"
] | 938f3fbb15af7e34e78490fabfe40110fd1b53ce97993e755ab43f08b928d620 |
"""Emojione autogen.
Generated from emojione source. Do not edit by hand.
MIT license.
Copyright (c) http://www.emojione.com
"""
version = "v2.2.7"
name = "emojione"
emoji = {
":100:": {
"category": "symbols",
"name": "hundred points symbol",
"unicode": "1f4af"
},
":1234:": {
... | facelessuser/sublime-markdown-popups | st3/mdpopups/pymdownx/emoji1_db.py | Python | mit | 259,076 | [
"CRYSTAL",
"FLEUR",
"Octopus"
] | 287d39a543b6cdf6aa4ed82fb3ca79e49cb6eef8210a5fc02e47007e6ccd6744 |
'''Convert to and from Roman numerals
This program is part of 'Dive Into Python 3', a free Python book for
experienced programmers. Visit http://diveintopython3.org/ for the
latest version.
'''
import re
class OutOfRangeError(ValueError): pass
class NotIntegerError(ValueError): pass
class InvalidRomanNumeralError(Va... | ctasims/Dive-Into-Python-3 | examples/roman9.py | Python | mit | 3,731 | [
"VisIt"
] | 94aa6c196a2781a597f48d0fbf9e44bf42ee37c1b7467d59dcef5d709d9b23b0 |
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