text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
############################################################################
##
## 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/tf_widget.py | Python | bsd-3-clause | 21,456 | [
"VTK"
] | 3a13493add6bc8281b23ad3f7e16e701c88fb327c64b41481ea93512eb571119 |
from __future__ import print_function
#import multiprocessing, os
#cpu = str(multiprocessing.cpu_count())-1
#os.environ['OPENBLAS_NUM_THREADS']=cpu
#os.environ['NUMBA_NUM_THREADS']=cpu
#os.environ['OMP_NUM_THREADS']=cpu
import timeit
from ImageD11 import cImageD11, sparseframe
import numpy as np, fabio, h5py, os
imp... | jonwright/ImageD11 | sandbox/bgfilter_grab.py | Python | gpl-2.0 | 7,220 | [
"Gaussian"
] | 4862301fc89a3ad23f10604c605b51387e081269cbc11921a9c53129c03a7b06 |
"""Work with Broad's Java libraries from Python.
Picard -- BAM manipulation and analysis library.
GATK -- Next-generation sequence processing.
"""
from contextlib import closing
from distutils.version import LooseVersion
import re
import sys
import os
import subprocess
import toolz as tz
from bcbio import utils
... | brainstorm/bcbio-nextgen | bcbio/broad/__init__.py | Python | mit | 21,920 | [
"Bioconda"
] | 3d570490ce4c53ffb341e40d49ec3fbec321efc0e8e32797e465f5f2bd2ccbb1 |
#! /usr/bin/env python
# coding=utf-8
"""A module containing routines for setting up simple friction simulations.
"""
# get Pysic - this is the package that handles atomic interactions
# see http://thynnine.github.io/pysic/
import pysic
# get some components of ASE - this is the package that handles dynamics
# see ht... | EinariTuukkanen/friction-simulation | friction_tools.py | Python | mit | 83,025 | [
"ASE"
] | 060bdb89bf039cedec787e92166f349e4b81b8622ca31e353122ca0b52d86896 |
# List Splunk Deployment Server Applications
# For use with Munk - Maltego for Splunk
# Author: Brian Warehime @nulltr0n
# 9/6/2014
# Importing various modules
from MaltegoTransform import *
import subprocess
import sys
import ConfigParser
import os
import xml.etree.cElementTree as ET
# Configuration Parser to grab ... | brianwarehime/munk | transforms/listdeploymentapps.py | Python | gpl-2.0 | 2,746 | [
"Brian"
] | 079664586f55e732bafa3265c33dfe9429cabd8f267412a97753fe9da61c40ac |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
from DIRAC import gLogger, S_OK
from DIRAC.Core.Base.AgentModule import AgentModule
from DIRAC.StorageManagementSystem.Client.StorageManagerClient import StorageManagerClient
from DIRAC.Res... | ic-hep/DIRAC | src/DIRAC/StorageManagementSystem/Agent/RequestPreparationAgent.py | Python | gpl-3.0 | 11,779 | [
"DIRAC"
] | 2b3007cb263ea7aedaac997b7d2b7bca2857827033e7265c608c6eb142baa706 |
"""This file implements the functionalities of a minitaur using pybullet.
"""
import os, inspect
currentdir = os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe())))
parentdir = os.path.dirname(os.path.dirname(currentdir))
os.sys.path.insert(0, parentdir)
import collections
import copy
import math
... | MadManRises/Madgine | shared/bullet3-2.89/examples/pybullet/gym/pybullet_envs/minitaur/envs/minitaur.py | Python | mit | 40,294 | [
"Gaussian"
] | e63cc4a271c77fe82553fd51264b2cf0fe16476e23097ad8dfa3c9870bdf6d1d |
# -*- coding: utf-8 -*-
import datetime
from south.db import db
from south.v2 import DataMigration
from django.db import models
class Migration(DataMigration):
def forwards(self, orm):
""" This migration looks at the skeletonlist_dashboard table to convert
it into an annoation of all it's entries.... | htem/CATMAID | django/applications/catmaid/migrations/0020_turn_skeletonlists_into_annotations.py | Python | agpl-3.0 | 47,800 | [
"NEURON"
] | a662661557f9f939d55b120b2d9151935112d12d2343d136c1a701c727c1d3c8 |
from __future__ import division, print_function
import sys
sys.path.append("../lib")
import logging
import theano
import theano.tensor as T
from theano import tensor
from blocks.bricks.base import application, lazy
from blocks.bricks.recurrent import BaseRecurrent, recurrent
from blocks.bricks import Random, Initia... | drewlinsley/draw_classify | draw/draw_cnn.py | Python | mit | 19,229 | [
"Gaussian"
] | 349c67d88656a836815c23139140501d98c3495d2733b96dbf4d23d17f99a35b |
#!/bin/env python
""" Show request given its ID, a jobID or a transformation and a task """
__RCSID__ = "$Id: $"
import datetime
def convertDate( date ):
try:
value = datetime.datetime.strptime( date, '%Y-%m-%d' )
except:
pass
try:
value = datetime.datetime.utcnow() - datetime.timedelta( hours = int(... | miloszz/DIRAC | RequestManagementSystem/scripts/dirac-rms-show-request.py | Python | gpl-3.0 | 6,870 | [
"DIRAC"
] | 95cc2faae298deb8007b68ad4a9dd0c703dbd6c7dc78684f9e50bff43e6830ac |
# -*- coding: utf-8 -*-
import os
import random
import numpy
import scipy
import scipy.ndimage
import nibabel
from core.toad.generictask import GenericTask
from lib.images import Images
from lib import util, mriutil
__author__ = "Mathieu Desrosiers"
__copyright__ = "Copyright (C) 2014, TOAD"
__credits__ = ["Mathieu... | mathieudesro/toad | tasks/02-parcellation.py | Python | gpl-2.0 | 15,835 | [
"VTK"
] | fb0e64e2ec6dd23a3ae3956cdb5ddb0d37aa7242d4a421f047bc8af4b9ae3faf |
import os
import sys
import numpy as np
import json
import logging
import re
import matplotlib.pyplot as plt
import matplotlib.patches as mpatches
back_path = os.path.abspath(os.path.join(os.getcwd(), os.pardir))
sys.path.append(os.path.join(back_path,
"Dionysus-python3/build/bindings/... | abulak/TDA-Cause-Effect-Pairs | Results.py | Python | gpl-2.0 | 14,291 | [
"Gaussian"
] | dc3a067940621216b7e7529dde9b4a764fe5e5103d435b229fe5bac35481d37f |
#
# GFSK modulation and demodulation.
#
#
# Copyright 2005-2007,2012 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# GNU Radio is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either v... | Gabotero/GNURadioNext | gr-digital/python/gfsk.py | Python | gpl-3.0 | 11,469 | [
"Gaussian"
] | 0a7cb4b3cb79fbf333f00d1cc508f4aabc0a347c6c06dcbdab180d5ff54f978d |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import time
# !! This is the configuration of Nikola. !! #
# !! You should edit it to your liking. !! #
# ! Some settings can be different in different languages.
# ! A comment stating (translatable) is used to denote those.
# ! There are two ways to... | njgraham/nathangraham.info | conf.py | Python | mit | 29,844 | [
"VisIt"
] | 78a2f509b9bd70d9827e2846bb02473eb546b8307ba7fe1677cccda71e0c91db |
# -*- coding: utf-8 -*-
"""
/***************************************************************************
Segreg
A QGIS plugin
This plugin computes spatial and non spatial segregation measures
-------------------
begin : 2017-01-25
... | sandrofsousa/Segreg | segreg.py | Python | gpl-2.0 | 32,506 | [
"Gaussian"
] | f5ac38f90083ed938cc2d8396a7ccfc6bd9ef9938f82197efd7133eebc302293 |
from netCDF4 import Dataset, MFDataset, num2date
from datetime import datetime as dt
import logging
import os
from os import path, rename
import requests
LOGGER = logging.getLogger("PYWPS")
# from esgf_utils import ATTRIBUTE_TO_FACETS_MAP
class CookieNetCDFTransfer:
def __init__(self, request, opendap_hostnames=... | bird-house/flyingpigeon | flyingpigeon/nc_utils.py | Python | apache-2.0 | 28,868 | [
"NetCDF"
] | 104de8b630d48cfb0d4ab74c053bf18551bc34e68ef783cdcb0d18dbad881c32 |
#
# Copyright 2010-2016 Universidad Complutense de Madrid (Spain)
#
# This file is part of Megara Exposure Time Calculator
#
# Megara ETC 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... | abouquin/django-megaraetc | etc/numeric.py | Python | gpl-3.0 | 39,596 | [
"Gaussian"
] | 72b3adad9c48829d4e0b6def3dbb2197cb26b384b492edafd36d9c7e9768aece |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | amjames/psi4 | psi4/share/psi4/databases/BAKERJCC93.py | Python | lgpl-3.0 | 42,456 | [
"Psi4"
] | 0e82a40472e1bedf325a2c6768659c879c02083fd3cfedf0b29593e6cfb626e9 |
#! /usr/bin/env python2
# -*- coding: utf-8 -*-
#
# This file is part of the Bacterial and Archaeal Genome Analyser
# Copyright (C) 2015-16 David Williams
# david.williams.at.liv.d-dub.org.uk
# License GPLv3+: GNU GPL version 3 or later
# This is free software: you are free to change and redistribute it
# There is NO W... | daveuu/baga | Repeats.py | Python | gpl-3.0 | 146,382 | [
"BWA",
"Biopython",
"pysam"
] | 1c46c512a6357b85c4c8c58400120c569efe9781435a8cc461652400c3a99025 |
# -*- coding: utf-8 -*-
# This file is part of KTBS <http://liris.cnrs.fr/sbt-dev/ktbs>
# Copyright (C) 2011-2012 Pierre-Antoine Champin <pchampin@liris.cnrs.fr> /
# Françoise Conil <francoise.conil@liris.cnrs.fr> /
# Universite de Lyon <http://www.universite-lyon.fr>
#
# KTBS is free software: you can ... | ktbs/ktbs | utest/test_ktbs_engine.py | Python | lgpl-3.0 | 38,653 | [
"ASE"
] | 7dbabb3b23482fd372f9d06f5504feef18718cf90bb455b8c1cae764822f38b6 |
# -*- 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 'ImmunizationHistory.tetanus_toxoid2'
db.delete_column(u'patient_immunizationhistory', 'tet... | aazhbd/medical_info01 | patient/migrations/0016_auto__del_field_immunizationhistory_tetanus_toxoid2__del_field_immuniz.py | Python | bsd-3-clause | 30,209 | [
"VisIt"
] | 9200897a161bf1b2003e5002aa64d6cb63215b9b6d1a1c0fd5a56d913a99d92a |
# -*- coding: utf-8 -*-
import pytest
from ..parsing import (
formula_to_composition,
formula_to_html,
formula_to_latex,
formula_to_unicode,
parsing_library,
to_reaction,
)
from ..testing import requires
@requires(parsing_library)
def test_formula_to_composition():
assert formula_to_comp... | bjodah/aqchem | chempy/util/tests/test_parsing.py | Python | bsd-2-clause | 9,048 | [
"CRYSTAL",
"ChemPy"
] | d2051c8340dc4065a10661d2ddb3f2ff57a41f4c4a9edc3785106eec0590f8f3 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import datetime
from django.core.exceptions import ImproperlyConfigured
from django.test import TestCase, override_settings
from django.utils.encoding import force_str
from django.views.generic.base import View
from .models import Artist, Author, Book, ... | frishberg/django | tests/generic_views/test_list.py | Python | bsd-3-clause | 12,120 | [
"MOOSE"
] | d92077bf4084d9b91fdd102ba59b2001eb4c1d988940b1a367c1bd29f3a280f3 |
#######################################################################
# This file is part of Lyntin.
# copyright (c) Free Software Foundation 2001, 2002
#
# Lyntin is distributed under the GNU General Public License license. See the
# file LICENSE for distribution details.
# $Id: event.py,v 1.9 2004/03/30 00:22:00 w... | v-legoff/accertin | lyntin/event.py | Python | gpl-3.0 | 4,948 | [
"exciting"
] | b1ed2769ba21e935834afe98dd8dc2fc04444fe1ea10ce16964413d7b282923b |
""" This is the guy that parses and interprets the local configuration options
"""
__RCSID__ = "$Id$"
import sys
import os
import getopt
import DIRAC
from DIRAC import gLogger
from DIRAC import S_OK, S_ERROR
from DIRAC.ConfigurationSystem.Client.ConfigurationData import gConfigurationData
from DIRAC.ConfigurationSy... | andresailer/DIRAC | ConfigurationSystem/Client/LocalConfiguration.py | Python | gpl-3.0 | 18,105 | [
"DIRAC"
] | 9fc80962b510619b27ca8fccb5a991d6916e7d772f40ce5a20cdce429ea2eabc |
""" core implementation of testing process: init, session, runtest loop. """
from __future__ import absolute_import, division, print_function
import contextlib
import functools
import os
import pkgutil
import six
import sys
import _pytest
from _pytest import nodes
import _pytest._code
import py
from _pytest.config i... | asajeffrey/servo | tests/wpt/web-platform-tests/tools/third_party/pytest/src/_pytest/main.py | Python | mpl-2.0 | 20,405 | [
"VisIt"
] | b4f1489c5d4b81d417c2049ea21f16de7901eadcafed72f473ce4194fa1a0210 |
# -*- coding: utf-8 -*-
"""Strongly connected components.
"""
# Copyright (C) 2004-2016 by
# Aric Hagberg <hagberg@lanl.gov>
# Dan Schult <dschult@colgate.edu>
# Pieter Swart <swart@lanl.gov>
# All rights reserved.
# BSD license.
import networkx as nx
from networkx.utils.decorators import not_implemen... | SanketDG/networkx | networkx/algorithms/components/strongly_connected.py | Python | bsd-3-clause | 11,932 | [
"VisIt"
] | 053809086f9edbe464d635fa80ec3c4607a00116b7c6d0c270c27c595cb1d96b |
import re
import warnings
from datetime import datetime
from distutils.version import LooseVersion
from functools import partial
import numpy as np
import pandas as pd
from pandas.errors import OutOfBoundsDatetime
from ..core import indexing
from ..core.common import contains_cftime_datetimes
from ..core.formatting i... | xray/xray | xarray/coding/times.py | Python | apache-2.0 | 16,133 | [
"NetCDF"
] | 834386f4f7e090aa128167b3330504577ced54b72fbc3b2454722b4c359cf6db |
# Version: 0.10+
"""
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner (modified by Florian Wilhelm and Felix Wick)
* License: Public Domain
* Compatible With: python2.6, 2.7, and 3.2, 3.3
[![Build Status](https://travis-ci.org/warner/py... | lenarother/pyhome | versioneer.py | Python | bsd-3-clause | 36,147 | [
"Brian"
] | 1fa24800cfe15a8dc53de8be4bec80a82319be1edaa47e8c890c547b94fc8797 |
"""
This module is a wrapper for Scientific.Visualization.VMD to make it work at
my machine... only classes Scene and SceneFile were modified.
"""
from Scientific.IO.TextFile import TextFile
from Scientific.Geometry import Transformation, Vector, VectorModule
import Numeric
import os, string, sys, tempfile
from Scient... | navjeet0211/Mara | Visualise/vmd.py | Python | gpl-2.0 | 2,978 | [
"VMD"
] | 4d00ad408d04df40def03bf5088354cb4e8833235f54ed8fd8d0b0543b341c59 |
## Convert PDB files to a pickled PDBModel object.
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2018 Raik Gruenberg & Johan Leckner
##
## This program is free software; you can redistribute it and/or
## modify it under the terms of the GNU General Public License as
## ... | graik/biskit | archive_biskit2/Biskit/StructureSlave.py | Python | gpl-3.0 | 4,168 | [
"Amber"
] | d4982ab92065edf0f69a9c5b8d586589870949a22c991ee8b18b7497adb90cd3 |
#!/usr/bin/env python
"""graph_utils.py: Graph related utilties. It does not require networkx library.
It writes files to be used with graphviz.
Last modified: Fri Mar 13, 2015 06:08PM
"""
__author__ = "Dilawar Singh"
__copyright__ = "Copyright 2013, NCBS Bangalore"
__credits__ = ["NC... | dilawar/moose-full | moose-core/python/moose/backend/graphviz.py | Python | gpl-2.0 | 13,068 | [
"MOOSE"
] | 86b8206cfb7454e941ddd765988e54b3605307bd30a711a7ea989ad5820300b9 |
import tensorflow as tf
import numpy as np
from skimage.segmentation import quickshift as skimage_quickshift
RATIO = 1.0
KERNEL_SIZE = 5
MAX_DISTANCE = 10
SIGMA = 0.0
def quickshift(image, ratio=RATIO, kernel_size=KERNEL_SIZE,
max_distance=MAX_DISTANCE, sigma=SIGMA):
"""Segments an image using qu... | rusty1s/graph-based-image-classification | segmentation/algorithm/quickshift.py | Python | mit | 2,913 | [
"Gaussian"
] | b245e1608d6c293a9066d4acf66dbfa709fa94231c7e83e330092b4d92855574 |
"""
This class is a helper to create the proper index and insert the proper values....
"""
from DIRAC.MonitoringSystem.Client.Types.BaseType import BaseType
__RCSID__ = "$Id$"
########################################################################
class WMSHistory( BaseType ):
"""
.. class:: WMSMonitorType
... | andresailer/DIRAC | MonitoringSystem/Client/Types/WMSHistory.py | Python | gpl-3.0 | 1,334 | [
"DIRAC"
] | 144f0e229ad858e84dd0f1225574ca8e13b9cb6c2a9093b03245579fb128b2ae |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# Author: Dejan Petelin <dejan [five] elin [at] gmail [dot] com>
# (based on GPML MATLAB Toolbox, version 3.2)
# Licence: BSD 3 clause
"""
The :mod:`sklearn.gpml` module implements Gaussian Process
based predictions.
"""
from .gp import GP
from . import cov
from . im... | depet/scikit-learn | sklearn/gpml/__init__.py | Python | bsd-3-clause | 440 | [
"Gaussian"
] | 602217379c9a539729b94f472ba63740c1c7d5775eb48f6a59ff72efd6a9b2ac |
#!/usr/bin/env python
#import argparse
#from glob import glob
#-s test_normalsamples.txt
#-b /mnt/lfs2/hend6746/devils/reference/sarHar1.fa
#-i /mnt/lfs2/hend6746/devils/reference/
from os.path import join as jp
from os.path import abspath
import os
import sys
import argparse
parser = argparse.ArgumentParser()
parse... | shendri4/devil_wgs | bam2vcf_GATK_Devils.py | Python | apache-2.0 | 3,295 | [
"BWA"
] | 8296cb6e48d5c73b52b85090ef7590a9f530c1b38974208e6688193d9fa12a4b |
from octopus.core import app, initialise
from octopus.lib import plugin, cli
import sys
command = sys.argv[1]
args = sys.argv[2:]
for name, path in app.config.get("CLI_SCRIPTS", {}).iteritems():
ran = False
if name == command:
# get an instance of the script
klazz = plugin.load_class(path)
... | JiscPER/magnificent-octopus | octopus/bin/run.py | Python | apache-2.0 | 746 | [
"Octopus"
] | faeabe7adb0fbbc5df52dd64ca103f7de58455dce08962cacff430acb41b39ca |
"""
Big California Districts. Districts with more than 10,000 students in the 2009-2010 year
"""
ca_big_dist = {
'0622710': 'Los Angeles Unified',
'0634320': 'San Diego Unified',
'0622500': 'Long Beach Unified',
'0614550': 'Fresno Unified',
'0612330': 'Elk Grove Unified',
'0635310': 'Santa Ana... | blargony/segrete | filters/ca_big.py | Python | mit | 7,259 | [
"Elk"
] | c3e31545fe87580b82711713c9c214fac2593a80c10385579a8a90d9dfb7601b |
# pylint: disable=missing-docstring
# pylint: disable=redefined-outer-name
from lettuce import world, step
from nose.tools import assert_false, assert_equal, assert_regexp_matches
from common import type_in_codemirror, press_the_notification_button, get_codemirror_value
KEY_CSS = '.key h3.title'
DISPLAY_NAME_KEY = "C... | solashirai/edx-platform | cms/djangoapps/contentstore/features/advanced_settings.py | Python | agpl-3.0 | 5,054 | [
"VisIt"
] | 552e39036c13d37b475bc5f1d07708e1b0dd8766dbcf762d5893d9d86000b64c |
from rest_framework import serializers
from elixir.models import *
from elixir.validators import *
class DownloadSerializer(serializers.ModelSerializer):
url = serializers.CharField(allow_blank=False, validators=[IsURLFTPValidator], required=True)
type = serializers.CharField(allow_blank=True, max_length=300, min_le... | bio-tools/biotoolsregistry | backend/elixir/serialization/resource_serialization/download.py | Python | gpl-3.0 | 1,930 | [
"Galaxy"
] | 95d1e5c375fd9862d4654ae3c8988c27660fa0469ce9f152472246d656c391c0 |
'''
This is our main file
'''
import random
from Player import Player
def intro(): #intro to the GAME
print('Good morning')
input('What a weird dream you woke from, huh? PRESS ENTER')
input('Maybe once you open your eyes ... PRESS ENTER')
input('You will see something IS a little off ... PRESS ENTER')... | blkFinch/hutch-val-pair-project | AdventureGameMain.py | Python | mit | 6,122 | [
"BWA"
] | 44eb238d8427b728f82a29f5e52e77bb15d77795e2e127eec08c7b1b8e7dacec |
# Benchmark the counting of alanine residues in a PDB file
import time
import MDAnalysis as mda
pdb_filepath = "data/1AKE.pdb"
u = mda.Universe(pdb_filepath)
def count():
return (u.residues.resnames == "ALA").sum()
start = time.time()
count()
end = time.time()
print(end - start)
| jgreener64/pdb-benchmarks | MDAnalysis/count.py | Python | mit | 289 | [
"MDAnalysis"
] | 7c40ee2caf92e6869da43e7e3232ea8e8c7b92ffce81cd82f2691f40db553e9b |
# Copyright (C) 2003-2005 Peter J. Verveer
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# 1. Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following d... | Universal-Model-Converter/UMC3.0a | data/Python/x86/Lib/site-packages/scipy/ndimage/tests/test_ndimage.py | Python | mit | 206,192 | [
"Gaussian"
] | 6a8a1350f618d8baf007951c4114d6c053194d62cdafa1f021622c0f8aa7f8b5 |
#!/usr/bin/env python
from __future__ import print_function
# xyz,atom,charge,spin = io.ReadMol(FileName)
# xyz,atom,charge,spin = io.ReadXYZ(FileName)
# io.OrcaIn(keywords,atom,xyz,charge,spin)
###################################################
# Subroutines
# generate backbones (linear and bran... | jmargraf/agrippa | DFfit/mol_io.py | Python | gpl-3.0 | 3,136 | [
"ORCA"
] | e3e84f196e5abead27f32ada2a68d8979c0d36152806b3c519575bb8b8bcfd69 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | fweik/espresso | samples/lb_profile.py | Python | gpl-3.0 | 2,787 | [
"ESPResSo"
] | 87480de61a693482ac974c856450d3249866e87d3a32501866d0eaacb857cfb0 |
# Copyright (c) 2020 Ultimaker B.V.
# Uranium is released under the terms of the LGPLv3 or higher.
import ast
# noinspection PyUnresolvedReferences
import base64 # Imported here so it can be used easily by the setting functions.
import builtins # To check against functions that are built-in in Python.
# noinspection... | Ultimaker/Uranium | UM/Settings/SettingFunction.py | Python | lgpl-3.0 | 12,842 | [
"VisIt"
] | 452f5dde4a0e370a98e2cfbabb8389267aff6cf4505929469cc894f1355b7b4b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# LICENSE: see LICENSE file
#
# bbs mode:
# You must rewrite Download,GetCurrentDir,CheckThreadsValid,
# GetThreadUrl and GetTitle function.
# single-page mode:
# You must rewrite Download function.
import sys
import logging
import os
import os.path
import requests
impo... | KanagiMiss/MoeDownloader | catch.py | Python | mit | 30,718 | [
"MOE"
] | 72556c593f4c4d4df401cadb76d1ade16fe951d207b7d6c97889c4c9858b041e |
from __future__ import print_function
from __future__ import unicode_literals
import io
import logging
import geolocation
import datetime
import dateutil
def create_strings(events):
"""
Formats the event tuples into a string that can be written to a file.close
Parameters
----------
events: Dicti... | paktor132/phoenix_pipeline | postprocess.py | Python | mit | 16,803 | [
"BWA"
] | e6c8f8aa70a774bc286d87f9d7244f4a31072e3f88f42a62f8af801e4569f0db |
from moose import *
import numpy as np
import networkx as nx
from collections import Counter
def xyPosition(objInfo,xory):
try:
return(float(element(objInfo).getField(xory)))
except ValueError:
return (float(0))
def setupMeshObj(modelRoot):
''' Setup compartment and its members pool,reacti... | dilawar/moose-full | moose-gui/plugins/kkitOrdinateUtil.py | Python | gpl-2.0 | 9,782 | [
"MOOSE"
] | 601409a5879e297ba254857af33a13fae76c07b74111975fb3563ff7bdee77de |
#!/usr/bin/env python
# Family size distribution of tags which were aligned to the reference genome
#
# Author: Monika Heinzl & Gundula Povysil, Johannes-Kepler University Linz (Austria)
# Contact: monika.heinzl@edumail.at
#
# Takes at least one TABULAR file with tags before the alignment to the SSCS,
# a BAM file wit... | loraine-gueguen/tools-iuc | tools/fsd/fsd_regions.py | Python | mit | 11,924 | [
"pysam"
] | e6ed0be68b26bb3f2d7750c5e9aa663bab6641894919c305142c591c42588365 |
# -*- coding: utf-8 -*-
# MolMod is a collection of molecular modelling tools for python.
# Copyright (C) 2007 - 2019 Toon Verstraelen <Toon.Verstraelen@UGent.be>, Center
# for Molecular Modeling (CMM), Ghent University, Ghent, Belgium; all rights
# reserved unless otherwise stated.
#
# This file is part of MolMod.
#
#... | molmod/molmod | molmod/io/cp2k.py | Python | gpl-3.0 | 13,374 | [
"CP2K"
] | 6c82956bcacd4ee9c7a195fa035c3569f44bc90510ec04bfa6c7b5db9b0032a0 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | rdipietro/tensorflow | tensorflow/python/ops/template.py | Python | apache-2.0 | 12,411 | [
"VisIt"
] | a37340439c5c7510ee0a337c2d910aae41ee35a2c3e4e78ef3e510f213d610a9 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""NBody in N^2 complexity
Note that we are using only Newtonian forces and do not consider relativity
Neither do we consider collisions between stars
Thus some of our stars will accelerate to speeds beyond c
This is done to keep the simulation simple enough for teaching purpo... | dikujepsen/OpenTran | matlab/NBody/NBodyPy/nbodyphysics_original.py | Python | mit | 2,000 | [
"Galaxy"
] | 52351ac138f58d7654802c04a95b41e862dd436ab34da0aecb0b9a93e6c5b94c |
import sys
import logging
from typing import Union
import numpy as np
import jax
import jax.numpy as jnp
from evojax.algo.base import NEAlgorithm
from evojax.util import create_logger
class OpenES(NEAlgorithm):
"""A wrapper around evosax's OpenAI Evolution Strategies.
Implementation:
https://github.com/... | google/evojax | evojax/algo/open_es.py | Python | apache-2.0 | 4,712 | [
"Gaussian"
] | 64381161e79f858554a64a33a922a738a9cffb5740ec2ef2af89cfba4087240a |
# coding: utf-8
"""Database querying methods for compound groups."""
import logging
from pandas import DataFrame
# import rdkit
# from rdkit import Chem, rdBase
# from rdkit.Chem import AllChem, Draw, rdqueries, rdMolDescriptors
from sqlalchemy import select, column, table, text # and_, or_, not_
from commongrou... | akokai/commongroups | commongroups/query.py | Python | mit | 5,322 | [
"RDKit"
] | 6dc2c00bbec89b1c7382c0a3d80aefdfff94351dd27813a43c75b2cfed4fb260 |
#!/usr/bin/env python
# coding: utf-8
import numpy as np
import os
import subprocess
import glob
import matplotlib.pyplot as plt
def tail(f, n, offset=0):
cmd = ["tail", "-n", str(n), f]
tail_output = subprocess.check_output(cmd)
tail_output.split('\n')
return lines
dirnam = '.'
output_files = glob... | seismology/mc_kernel | UTILS/plot_timers.py | Python | gpl-3.0 | 2,984 | [
"NetCDF"
] | 9ff437c93c86c036f4fe2fc6abea4d9310089d26ad508e730e25ceb2580cf56b |
#
# This source file is part of appleseed.
# Visit https://appleseedhq.net/ for additional information and resources.
#
# This software is released under the MIT license.
#
# Copyright (c) 2014-2018 The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this s... | appleseedhq/blenderseed | preferences.py | Python | mit | 4,941 | [
"VisIt"
] | 0f7190140c66d32fa92112c10beb14eba4ddd484cad17669e7e8f906728ce426 |
# $Id$
#
# Copyright (C) 2007 greg Landrum
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
from __future__ import print_function
import unittest... | jandom/rdkit | rdkit/Chem/AtomPairs/UnitTestDescriptors.py | Python | bsd-3-clause | 3,601 | [
"RDKit"
] | 8d4d6dbcedc5a2653bf87d097e80bfb84076d2fd8f5e74d83f77d6c935735891 |
# Copyright (c) 2003-2010 LOGILAB S.A. (Paris, FRANCE).
# Copyright (c) 2009-2010 Arista Networks, Inc.
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
# 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
# ... | sloanyang/depends | third_party/pylint/checkers/base.py | Python | gpl-2.0 | 33,121 | [
"VisIt"
] | e4336e002c845101cb8450b2cdc5e6632a2165da6d5c6584e143e18c78ae4bba |
import numpy as np
from sklearn.base import BaseEstimator, RegressorMixin
from scipy import linalg
from sklearn.utils import check_array
import matplotlib.pyplot as plt
def plot_gp_confidence(gp, show_gp_points=True, X_low=-1, X_high=1, X_step=.01, xlim=None, ylim=None):
xpts = np.arange(X_low, X_high, step=X_ste... | kastnerkyle/gp2 | gp2/gaussian_process.py | Python | bsd-3-clause | 2,978 | [
"Gaussian"
] | bc556cef2be8a62059902bcdfb1659e56a6dedd942e476d434fdd97a5972acfd |
# encoding: 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):
# Removing unique constraint on 'GeoLevel', fields ['name']
db.delete_unique(u'profiles_geolevel', ['name'... | ProvidencePlan/Profiles | communityprofiles/profiles/oldmigrations/0062_auto__del_unique_geolevel_name.py | Python | mit | 20,749 | [
"MOE"
] | 3b68a259dfd2979e6eba767b91df9ea4a6b8f544e13f0637f53d2e1724261358 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright 2014 The Plaso Project Authors.
# Please see the AUTHORS file for details on individual 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 L... | cvandeplas/plaso | plaso/parsers/cookie_plugins/ganalytics_test.py | Python | apache-2.0 | 5,833 | [
"VisIt"
] | b0e18c5cc6a534366ebf6cab727bfd9293ba1a915dcd7720fa814a97060d1df6 |
"""Base class for mixture models."""
# Author: Wei Xue <xuewei4d@gmail.com>
# Modified by Thierry Guillemot <thierry.guillemot.work@gmail.com>
# License: BSD 3 clause
from __future__ import print_function
import warnings
from abc import ABCMeta, abstractmethod
from time import time
import numpy as np
from .. impor... | altairpearl/scikit-learn | sklearn/mixture/base.py | Python | bsd-3-clause | 14,799 | [
"Gaussian"
] | 40d58bec7a4a46cccae582968c5dd7f8cd2f96a92198f1de69f7daa3307a9ff5 |
# (c) Nelen & Schuurmans. GPL licensed, see LICENSE.rst.
# Base Django settings, suitable for production.
# Imported (and partly overridden) by developmentsettings.py which also
# imports localsettings.py (which isn't stored in svn). Buildout takes care
# of using the correct one.
# So: "DEBUG = TRUE" goes into devel... | nens/krwlight | krwlight/settings.py | Python | gpl-3.0 | 6,879 | [
"BLAST"
] | 23c8dfa1729eb0f2b38f3fae1737e81cf8c570c238739513fb6bca9933398a32 |
"""
The following tools have been eliminated from the distribution:
Map with Bowtie for Illumina, Map with Bowtie for SOLiD, Lastz,
and Lastz paired reads. The tools are now available in the
repositories named bowtie_wrappers, bowtie_color_wrappers, lastz,
and lastz_paired_reads from the main Galaxy tool shed at
http:... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/tool_shed/galaxy_install/migrate/versions/0007_tools.py | Python | gpl-3.0 | 570 | [
"Bowtie",
"Galaxy"
] | 6826f1dfe107aca61b676e63ed08c1cdec0f711d15db39c544e69af56f24df0f |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | diffusion_distillation/diffusion_distillation/utils.py | Python | apache-2.0 | 10,773 | [
"Gaussian"
] | 9d7ea5bec67263a773b6aa00a27171e1b2ce59eee0f7fa9a4424723be0125181 |
import tomviz.operators
class LabelObjectDistanceFromPrincipalAxis(tomviz.operators.CancelableOperator):
def transform_scalars(self, dataset, label_value=1, principal_axis=0):
"""Computes the distance from the centroid of each connected component
in the label object with the given label_value to ... | cryos/tomviz | tomviz/python/LabelObjectDistanceFromPrincipalAxis.py | Python | bsd-3-clause | 3,934 | [
"VTK"
] | 839b1b577b594395f57a710af423e53154f7f2d3334b1d66f6f33eede0f0e14e |
# coding: utf-8
from __future__ import division, unicode_literals
"""
This module implements input and output processing from Nwchem.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep@gmail.com"
__date_... | yanikou19/pymatgen | pymatgen/io/nwchemio.py | Python | mit | 25,487 | [
"Gaussian",
"NWChem",
"pymatgen"
] | 043fc07bb7c533a9fd84411ca7b84d4d8da01ae9c445e53cccc9225621457e85 |
import os
import vtk
from vtk.test import Testing
import Tkinter
from vtk.tk.vtkTkRenderWindowInteractor import vtkTkRenderWindowInteractor
class TestTkRenderWindowInteractor(Testing.vtkTest):
# Stick your VTK pipeline here if you want to create the pipeline
# only once. If you put it in the constructor or... | berendkleinhaneveld/VTK | Rendering/Tk/Testing/Python/TestTkRenderWindowInteractor.py | Python | bsd-3-clause | 1,911 | [
"VTK"
] | c1a939df75585b9355146eb567a7142cd8e5d0f7e96fdb6807250f140545a54b |
"""
Kernel Density Estimation
-------------------------
"""
# Author: Jake Vanderplas <jakevdp@cs.washington.edu>
import numpy as np
from scipy.special import gammainc
from ..base import BaseEstimator
from ..utils import check_random_state
from ..utils.validation import _check_sample_weight, check_is_fitted
from ..ut... | manhhomienbienthuy/scikit-learn | sklearn/neighbors/_kde.py | Python | bsd-3-clause | 10,928 | [
"Gaussian"
] | 73daf46d2b3f7f810ea03f7a04ad57bd921740dc0e7138e05f247ea3e204eb6e |
import numpy as _np
import mdtraj as _md
try:
from sklearn.mixture import GaussianMixture as _GMM
except ImportError:
from sklearn.mixture import GMM as _GMM
# From pyemma's coordinates
from pyemma.coordinates import \
source as _source, \
cluster_regspace as _cluster_regspace, \
save_traj as _sav... | markovmodel/molPX | molpx/_bmutils.py | Python | lgpl-3.0 | 47,396 | [
"Gaussian",
"MDTraj"
] | a553a9c3b30c17e0efd4e7ca0ec7e754c5151c9f98a4b8a151280804ff729747 |
from _problem import cassini_1, gtoc_1,cassini_2, rosetta, messenger_full, tandem, laplace, sagas, mga_1dsm_alpha, mga_1dsm_tof, mga_incipit, mga_incipit_cstrs, mga_part
#from _problem import _gtoc_2_objective
# Redefining the constructors of all problems to obtain good documentation and allowing kwargs
def _cassin... | enikulenkov/PaGMO | PyGMO/problem/_gtop.py | Python | gpl-3.0 | 22,688 | [
"VisIt"
] | 38eb5992b42cc4b4f2c297ec4149413f67e32cc24249a879cd942aa07b70d99e |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | lothian/psi4 | psi4/driver/aliases.py | Python | lgpl-3.0 | 7,396 | [
"Psi4"
] | 9bf8ce24373f8ececad34f532923140c758c1762391c82bd36e74cf8c96f3e4d |
# -*- coding: utf-8 -*-
"""
:Created on: Tue Oct 2 15:10:46 2012
:author: Stuart Mumford
"""
import numpy as np
from mayavi import mlab
def set_text(text_property):
"""
Set the text to sane defaults
Parameters
----------
text_property: mayavi TextProperty object
"""
text_property.bol... | Cadair/scipy2014plotting | mayavi_plotting_functions.py | Python | bsd-2-clause | 7,941 | [
"Mayavi"
] | 647307609571ed63358add3aea6f48956549ab080b3a9d7fdedad00832bd16a9 |
#
# 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) 2014-2017 The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this s... | jasperges/blenderseed | properties/nodes/orennayar_brdf.py | Python | mit | 4,208 | [
"VisIt"
] | ebd8f645579ec1cde88ca274caf45452e51f36211f5c7c4264410694079787b2 |
#
# Copyright 2018 Analytics Zoo Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ... | intel-analytics/analytics-zoo | pyzoo/test/zoo/orca/automl/search/test_tensorboardlogger.py | Python | apache-2.0 | 2,041 | [
"ORCA"
] | a745136c14898a3d6d807f46ac16b2dae355f73a02371882cdc2d15d714dc4b3 |
#!/usr/bin/env python
import os
import sys
import json
import argparse
import numpy as np
import matplotlib
import multiprocessing
import logging
matplotlib.use('agg')
import matplotlib.pyplot as plt
from pychemia.code.abinit import AbinitInput, AbinitOutput
from pychemia.population.orbitaldftu import dmatpawu2params... | MaterialsDiscovery/PyChemia | scripts/OrbitalDFTU_Evaluator.py | Python | mit | 18,132 | [
"ABINIT",
"Firefly"
] | 11f0f3cd48181154ebf722d42a0fe6ea8ad220ce63aae07022aa6afab371bf83 |
import openvoronoi as ovd
import ovdvtk
import time
import vtk
import math
# draw a line from pt1 to pt2 with the given color
def drawLine(myscreen, pt1, pt2, lineColor):
myscreen.addActor(ovdvtk.Line(p1=(pt1.x, pt1.y, 0), p2=(pt2.x, pt2.y, 0), color=lineColor))
def drawLinesegs(myscreen, points, lines):
fo... | aewallin/openvoronoi | python_examples/offset/offset2vtk.py | Python | lgpl-2.1 | 10,278 | [
"VTK"
] | e44a0bbf8297e0822ec8d10b838c86b7a642ed3c1ff7b454c1833ee8ac453270 |
# ^_^ WEEK 03 FUN ^_^
# TAKE-HOME CHALLENGE
from tkinter import *
def draw(canvas, width, height):
# Fun: For more interesting colors, visit: http://wiki.tcl.tk/37701
fillColor = "blue"
canvas.create_rectangle(0, 0, 10, 10, fill=fillColor)
canvas.create_rectangle(10, 10, 20, 20, fill=fillColo... | google/teknowledge | curriculum/04_graphics_02_loops/04_02_02_fun_square_diagonals.py | Python | apache-2.0 | 1,025 | [
"VisIt"
] | 737cee7741341a082ffdeef1544990d4a7eac289403b302e968dbdc0ed37b43e |
""" Models for the shopping cart and assorted purchase types """
from collections import namedtuple
from datetime import datetime
from decimal import Decimal
import pytz
import logging
import smtplib
from boto.exception import BotoServerError # this is a super-class of SESError and catches connection errors
from dja... | XiaodunServerGroup/ddyedx | lms/djangoapps/shoppingcart/models.py | Python | agpl-3.0 | 27,310 | [
"VisIt"
] | 2036df8034b1a7388e4c5cd3971c4b384025fb3bbbc0394b8dd534a3d07732ac |
# -*- encoding:utf-8 -*-
import sys, os
sys.path.append(os.path.join(os.path.dirname(__file__), '..'))
from docscrape import NumpyDocString, FunctionDoc, ClassDoc
from docscrape_sphinx import SphinxDocString, SphinxClassDoc
from nose.tools import *
doc_txt = '''\
numpy.multivariate_normal(mean, cov, shape=None, sp... | hohe/scikit-rf | doc/sphinxext/tests/test_docscrape.py | Python | bsd-3-clause | 15,292 | [
"Gaussian"
] | 78bd35f259fccaa9b9f0dc8b43128a3174145fb4eee79a63eb0ea1c7585a24a5 |
import os
config = {
# This config file will be detected in production environment and values defined here will overwrite those in config.py
'environment': "production",
# webapp2 sessions
'webapp2_extras.sessions': {'secret_key': '-2{ZNAz&Cku/%{Gvx/yaUYl.*-}gol`QIMdr[_`L`[1dFvE+FV9,Juspb:b{zr-f'},
... | joshainglis/sa-tools | bp_content/themes/sa_default/config/production.py | Python | lgpl-3.0 | 2,824 | [
"VisIt"
] | e6ac353773f73a0fe4b1f9e6aa32d440e32863a0dcb6ae38da0c0ceb05ff84a6 |
#!/usr/bin/env python2
import os
import sys
import gtk
from ctypes import c_int
from PyQt5.QtCore import Qt, QSize, QUrl
from PyQt5.QtWebKitWidgets import QWebView
from PyQt5.QtWidgets import QApplication, QMessageBox
from WebLullaby import APP_NAME
class Browser(object):
def __init__(self, app, enable_user_int... | andras-tim/xscreensaver-web-lullaby | WebLullaby/__main__.py | Python | gpl-3.0 | 3,386 | [
"Galaxy"
] | 9ba32e69a3311c3fef88eca8a7a406c01e106b97eadaae119cd9d93a51765d1d |
from django.utils.translation import ugettext_lazy as _
'''
This file is a place to store static, translatable lists (or tuples!). Choice
lists for registration fields were the original application.
'''
SECTORS = (
# (value, human-readable label)
("Public Administration", _("Public Administration")),
("Ar... | awemulya/fieldsight-kobocat | onadata/apps/fieldsight/static_lists.py | Python | bsd-2-clause | 11,075 | [
"BWA"
] | 32b5a13bdc3f648d96def1edeffceaa3d3351835e58ed226f9631ea47e7671c3 |
'''IR code walker
'''
from __future__ import absolute_import
import itertools
from . import ir as I
class IRWalker(object):
'''depth first (by default) code walker
'''
def __init__(self):
self.dispatch_table = {}
def visit(self, node):
if node is not None:
return self.... | matthagy/Jamenson | jamenson/compiler/walk.py | Python | apache-2.0 | 4,032 | [
"VisIt"
] | 459e2a6e7c788988bb5a9a7b60cd6905f3f9adac03dd20280298d26b5855c6fa |
"""Matlab(tm) compatibility functions.
This will hopefully become a complete set of the basic functions available in
matlab. The syntax is kept as close to the matlab syntax as possible. One
fundamental change is that the first index in matlab varies the fastest (as in
FORTRAN). That means that it will usually pe... | fxia22/ASM_xf | PythonD/site_python/Numeric/MLab.py | Python | gpl-2.0 | 12,285 | [
"Gaussian"
] | 860644e455c037d45893be8530fc823634e3810777d0fa2e802670077a7a13f3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
copyright = """
Copyright 2008, 2009 Moritz Doll and Christian Scharkus
This file is part of rattlekekz.
rattlekekz 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 S... | Jem777/rattlekekz | rattlekekz/core/controller.py | Python | lgpl-3.0 | 32,874 | [
"VisIt"
] | 90d8086d6e9bf74bf4017b197a56c7886d82bc6b7599e1c3820e3426b7e51406 |
"Melting a copper cluster."
from numpy import *
from asap3 import Atoms, EMT, units
from ase.visualize.primiplotter import *
from ase.lattice.cubic import FaceCenteredCubic
from asap3.md.langevin import Langevin
# Create the atoms
atoms = FaceCenteredCubic(size=(5,5,5), symbol="Cu", pbc=False)
# Associate the EMT p... | auag92/n2dm | Asap-3.8.4/Examples/Melting.py | Python | mit | 1,345 | [
"ASE"
] | 6776c9d0d2b93c3a8dc74dbb93627497734922c43d5a7b792a71e10299048cb8 |
# c: 05.05.2008, r: 05.05.2008
import sys
sys.path.append( '.' )
from sfepy.fem.periodic import *
# c: 05.05.2008, r: 05.05.2008
def define_regions( filename ):
"""Define various subdomain for a given mesh file. This function is called
below."""
regions = {}
is3d = False
regions['Y'] = ('all'... | certik/sfepy | examples/rs_correctors.py | Python | bsd-3-clause | 9,269 | [
"VTK"
] | 94e3044abe1cca7741c1d33ac9d1f464b32968c4682ea7a22751a59009da6322 |
''' <h1>Library for combined x-ray and neutrons simulations.</h1>
<p> The neutron simulations is capable of handling non-magnetic,
magnetic non-spin flip as well as neutron spin-flip reflectivity.
The model works with scattering lengths densities directly.
</p>
<h2>Classes</h2>
<h3>Layer</h3>
<code> Layer(sld_n=0.0, sl... | haozhangphd/genx-py3 | genx/models/soft_nx.py | Python | gpl-3.0 | 24,287 | [
"Gaussian"
] | 256c96522afa34cd80fa01bb0728a681fef71acd3530a25f630bd044edda2139 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | anderspitman/scikit-bio | skbio/sequence/tests/test_genetic_code.py | Python | bsd-3-clause | 19,642 | [
"scikit-bio"
] | b5706fded0f06c85588e8ce3c69fdb8239f19494f3169f7f8e9b955c1b2d6267 |
import math
def erf(x):
# Python 2.7 defines math.erf(), but we need to cater for older versions.
a = 8 * (math.pi - 3) / (3 * math.pi * (4 - math.pi))
x2 = x * x
y = -x2 * (4 / math.pi + a * x2) / (1 + a * x2)
return math.copysign(math.sqrt(1 - math.exp(y)), x)
def erf_inv(x):
# Above erf f... | ianfab/variantfishtest | stat_util.py | Python | gpl-3.0 | 4,476 | [
"Gaussian"
] | 06af2f59cc22eb17213f67d243bafc0fb2e4bb6627026787ede9d4cf337387ea |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | goozbach/ansible | lib/ansible/utils/color.py | Python | gpl-3.0 | 3,218 | [
"Brian"
] | 2d58cfed47245494b7f5cb66c6f577f3a8b7568488374df58ed669d47e3dbd9d |
""" This module handles everything related to log parsing """
import re # For parsing the log file (regular expressions)
import os # For working with files on the operating system
import logging # For logging
from game_objects.item import Item
from game_objects.floor import Floor, Curse
from game_objects.... | Hyphen-ated/RebirthItemTrackerTest | src/log_parser.py | Python | bsd-2-clause | 11,504 | [
"GULP"
] | f50b954846c512876260f86431956a52a414a7a44da3f91426d004c9168a35b4 |
import numpy as np
from ase.constraints import FixAtoms
from ase.calculators.emt import EMT
from ase.neb import NEB
from ase.optimize.fire import FIRE as QuasiNewton
from ase.io import read
# Read the previous configurations
initial = read('N2.traj')
final = read('2N.traj')
# Make 9 images (note the use of copy)
co... | misdoro/python-ase | doc/tutorials/N2Cu-Dissociation2.py | Python | gpl-2.0 | 957 | [
"ASE"
] | 53f7d37617b6007c63354c17b817cc7a1c96bb6f959d749cf6b1e8de119bdedc |
# -*- coding: utf-8 -*-
from rdflib import Graph, URIRef, BNode
from rdflib.namespace import RDF
__all__ = ['parse']
def parse(page):
g = Graph()
g.parse(data=page, format="microdata")
places = ((s, schema(o)) for s, p, o in g.triples((None, RDF.type, None))
if is_place(o))
return [co... | rizsotto/Ente | ente/parser.py | Python | bsd-3-clause | 3,815 | [
"CASINO"
] | 5686b5d8171d7e78f2a5ddcd93df60341e0447f73e32e00cac07c184cdf44f28 |
""" DIRAC Notification Client class encapsulates the methods exposed
by the Notification service.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import six
from DIRAC import gLogger, S_ERROR
from DIRAC.Core.Base.Client import Cli... | ic-hep/DIRAC | src/DIRAC/FrameworkSystem/Client/NotificationClient.py | Python | gpl-3.0 | 4,912 | [
"DIRAC"
] | b6ed7fd21f21a14e44940b919980b34d3f813df8282f86c80e7db90204a84443 |
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------------
# Python Youtube API v1.0.0
# ---------------------------------------------------------------------------
# License: GPL (http://www.gnu.org/licenses/gpl-3.0.html)
# Based on code from php-youtube-api, https://github.... | LeeSoftRu/python-youtube-api | youtube_api/__init__.py | Python | gpl-3.0 | 9,797 | [
"VisIt"
] | b925c05bc3cc2f628beb53ea9252ac0fda0f2d1d2b631f8a51c1409b28d9d9c9 |
"""
local path implementation.
"""
from __future__ import with_statement
from contextlib import contextmanager
import sys, os, re, atexit, io
import py
from py._path import common
from py._path.common import iswin32
from stat import S_ISLNK, S_ISDIR, S_ISREG
from os.path import abspath, normpath, isabs, exists, isdir... | pdxwebdev/yadapy | yada/lib/python2.7/site-packages/py/_path/local.py | Python | gpl-3.0 | 32,118 | [
"VisIt"
] | 40c783e4391b0618942e5b9c2510769df2540cc1e037be4ce431c9ad5539e5be |
import os
import logging
import yaml
import copy
import operator
import requests
try:
unicode("hola")
except NameError:
unicode = str
try:
from urlparse import urlparse
except ImportError:
from urllib.parse import urlparse
from toscaparser.tosca_template import ToscaTemplate
from toscaparser.elements.... | indigo-dc/im | IM/tosca/Tosca.py | Python | gpl-3.0 | 65,647 | [
"Galaxy"
] | 08a416dce0569742c72ae71b512a25beb6a8ce6d95bc0e036d5b854837caede4 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.