text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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|---|---|---|---|---|---|---|---|
# coding: utf-8
from __future__ import division, unicode_literals
import re
import os
import shutil
import subprocess
from string import Template
from monty.io import zopen
from monty.json import MSONable
from pymatgen.core.structure import Molecule
"""
This module implements input and output processing for Fiesta... | aykol/pymatgen | pymatgen/io/fiesta.py | Python | mit | 28,804 | [
"NWChem",
"pymatgen"
] | a6101c5d77d4ec32966a379ff6cea53e3db9597d46ca4ba730b50ac7607f9c3b |
#!/usr/bin/env python
'''
setup board.h for chibios
'''
import argparse, sys, fnmatch, os, dma_resolver, shlex, pickle, re
import shutil
parser = argparse.ArgumentParser("chibios_pins.py")
parser.add_argument(
'-D', '--outdir', type=str, default=None, help='Output directory')
parser.add_argument(
'--bootloade... | akolobov/ardupilot | libraries/AP_HAL_ChibiOS/hwdef/scripts/chibios_hwdef.py | Python | gpl-3.0 | 56,480 | [
"CRYSTAL"
] | e726f071f071016c697d9fd19a272aa314209a64aa806d39c4e3e7130265e8e8 |
# pulsegen.py ---
#
# Filename: pulsegen.py
# Description:
# Author:Subhasis Ray
# Maintainer:
# Created: Sat Jun 23 10:26:25 2012 (+0530)
# Version:
# Last-Updated: Sat Jun 23 13:51:28 2012 (+0530)
# By: subha
# Update #: 34
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change log:
#... | BhallaLab/moose-examples | snippets/pulsegen.py | Python | gpl-2.0 | 1,827 | [
"MOOSE"
] | a3d73ea73bdd02596f8f3ccb098d1bd2e3ab49188687b0ecef061d8deb4b55a6 |
"""
Views for user API
"""
import json
from django.shortcuts import redirect
from django.utils import dateparse
from opaque_keys import InvalidKeyError
from opaque_keys.edx.keys import UsageKey
from rest_framework import generics, views
from rest_framework.decorators import api_view
from rest_framework.response import... | philanthropy-u/edx-platform | lms/djangoapps/mobile_api/users/views.py | Python | agpl-3.0 | 15,245 | [
"VisIt"
] | f547d602a5a57d90a57df6864f3e37c8a37fdbccb629565248522c0996ba28d6 |
#
# 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) 2019 Jonathan Dent, The appleseedhq Organization
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# ... | dictoon/blenderseed | translators/assethandlers.py | Python | mit | 5,118 | [
"VisIt"
] | bfdcab9af37872555f5709554547e770893f3adaf0d7bea625ee7bb29db7a58e |
#!/usr/bin/env python
import os
import re
import logging
import logging.config
import subprocess
import smtplib
import ConfigParser
from email.mime.multipart import MIMEMultipart
from email.mime.text import MIMEText
CONFIG = {}
IS_ERROR = None
logging.config.fileConfig(os.path.abspath(os.path.join(os.path.dirname(__... | bobbyromeo/mypihc | bin/common/utils.py | Python | mit | 9,207 | [
"VisIt"
] | cbb60cb75495b71542601aade55dc2910e526a93651702c1143a1911b38a7173 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | nburn42/tensorflow | tensorflow/contrib/autograph/pyct/static_analysis/type_info.py | Python | apache-2.0 | 8,937 | [
"VisIt"
] | 523cc0857a28bc8bd82a06e85eeeb5d0f1c0fa62145fa3f1412a030f5b4d24b8 |
# Licensed to the Apache Software Foundation (ASF) under one
# or more contributor license agreements. See the NOTICE file
# distributed with this work for additional information
# regarding copyright ownership. The ASF licenses this file
# to you under the Apache License, Version 2.0 (the
# "License"); you may not u... | kaiping/incubator-singa | test/python/test_tensor.py | Python | apache-2.0 | 8,726 | [
"Gaussian"
] | 487d0c2ebc4825dbc3475f55192ff0c52117b3b7e36e7badddba5a0945afb076 |
"""The extended KF (EKF) and the (Rauch-Tung-Striebel) smoother."""
import numpy as np
from dapper.tools.linalg import mrdiv
from dapper.tools.progressbar import progbar
from . import da_method
@da_method()
class ExtKF:
"""The extended Kalman filter.
If everything is linear-Gaussian, this provides the exa... | nansencenter/DAPPER | dapper/da_methods/extended.py | Python | mit | 3,584 | [
"Gaussian"
] | 6ecf0f3dc81e0e59971cc8e279c718c080f765488a2005bb7fafda9d8d4cc1c6 |
# Lint as: python3
# Copyright 2019 DeepMind Technologies Limited. 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
#... | deepmind/ferminet | ferminet/utils/scf.py | Python | apache-2.0 | 6,630 | [
"Gaussian",
"PySCF"
] | be16ef0fe330975ffd3cce3f5541c2664caac975150ebf165a1f41d2f9bbe5ee |
import pickle
from io import BytesIO
import numpy as np
import scipy.sparse
from sklearn.datasets import load_digits, load_iris
from sklearn.model_selection import train_test_split
from sklearn.model_selection import cross_val_score
from sklearn.externals.six.moves import zip
from sklearn.utils.testing import assert... | jaidevd/scikit-learn | sklearn/tests/test_naive_bayes.py | Python | bsd-3-clause | 19,944 | [
"Gaussian"
] | 6130f24ad9a03152be243eaf310ea336c08b406eaeec151ea75101beee14415b |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS Instructor Dashboard.
"""
import time
from flaky import flaky
from nose.plugins.attrib import attr
from bok_choy.promise import EmptyPromise
from ..helpers import UniqueCourseTest, get_modal_alert, EventsTestMixin
from ...pages.common.logout import LogoutPage
... | MakeHer/edx-platform | common/test/acceptance/tests/lms/test_lms_instructor_dashboard.py | Python | agpl-3.0 | 51,182 | [
"VisIt"
] | d172454e6864197da279b7d9b578e943039b53c82b87bf95c32148fc1403d210 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
###########################################################################
# #
# ESPResSo++ Python script for tabulated GROMACS simulation #
# ... | acfogarty/espressopp | testsuite/pi_water/water.py | Python | gpl-3.0 | 7,408 | [
"ESPResSo",
"Gromacs",
"VMD"
] | 1a259825e1ebddcf7c83dcaed6424595df0cbc114dd09b5e4eaf97dce3cc2209 |
#!/usr/bin/env python
#coding:utf-8
import os
from geopytool.ImportDependence import *
from geopytool.CustomClass import *
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
here = os.path.abspath(os.path.dirname(__file__))
try:
README = open(os.path.join(here, 'README... | chinageology/GeoPython | geopytool/setup.py | Python | gpl-3.0 | 1,809 | [
"VisIt"
] | 078bdb5ff850d77b5f7f2f26ee60f21bc130cc81279cd6559a8e1ffd492910ed |
import sys
sys.path.insert(1,"../../")
import h2o
from tests import pyunit_utils
import random
import os
def javapredict_dynamic_data():
# Generate random dataset
dataset_params = {}
dataset_params['rows'] = random.sample(range(5000,15001),1)[0]
dataset_params['cols'] = random.sample(range(10,21),1)[0... | madmax983/h2o-3 | h2o-py/tests/testdir_javapredict/pyunit_javapredict_dynamic_data_paramsDL.py | Python | apache-2.0 | 3,401 | [
"Gaussian"
] | 91ed203b7c3b62a93b9551b5c03048c19888d38db5ebc43ab99acd6e9d4fb056 |
#!/usr/bin/env python3
## INFO ########################################################################
## ##
## formbuilder ##
## =========== ... | petervaro/formbuilder | formbuilder.py | Python | gpl-3.0 | 3,680 | [
"VisIt"
] | 41f8e80632bb6c58628c0a85af5a704bc5c33f7d0180ff44301811b54d80e6a6 |
"""Collection of bulk systems.
From this paper:
Philipp Haas, Fabien Tran, Peter Blaha
Calculation of the lattice constant of solids with semilocal functionals
Phys. Rev. B 79, 085104 (2009)
dx.doi.org/10.1103/PhysRevB.79.085104
Data extracted to csv files with:
* lattice constant::
pdftotext -... | grhawk/ASE | tools/ase/test/tasks/htb.py | Python | gpl-2.0 | 18,943 | [
"ASE",
"CRYSTAL"
] | b4e870bf71d60f69011d789309843115d775cf5260640f80eb796c76f5f4ebda |
##
# Copyright 2013 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://vscentrum.be/nl/en),
# Flemish Research Foundation (FWO)... | wpoely86/easybuild-easyblocks | easybuild/easyblocks/d/dl_poly_classic.py | Python | gpl-2.0 | 2,179 | [
"DL_POLY"
] | 68cc22a71518fa5762455c8a8f70f47f21201cb502a2a51ac1e18b2e583d69ea |
#!/usr/bin/env python3
import concurrent.futures
import datetime
import functools
import io
import time
import urllib.parse
import curl # https://github.com/m13253/pycurl-python3
import danmaku2ass # https://github.com/m13253/danmaku2ass
import tornado.gen
import tornado.httpclient
import tornado.httpserver
impor... | m13253/danmaku2ass-bilidown-backend | bilidown-danmaku2ass.py | Python | gpl-3.0 | 9,336 | [
"VisIt"
] | 7d38c76cd1f1b3b6f98132a0ed9303f84d81179524b0d6b109abdfdb631fee17 |
"""
Definition of classes handling dispersion curves and
velocity maps (obtained by inverting dispersion curves)
"""
from seissuite.ant import pserrors, psutils
import itertools as it
import numpy as np
from scipy.optimize import curve_fit
from scipy.interpolate import interp1d
import os
import glob
import pickle
impo... | boland1992/SeisSuite | seissuite/ant/pstomo.py | Python | gpl-3.0 | 66,086 | [
"Gaussian"
] | ac2bac7214e60a608dcb46b5fa3f3f48098d2c744e2e6e3bb5f294f44cd8c37f |
# __RCSID__ = "$Id$"
#
# # FIXME: should be rewritten as a real unitttest
#
# import DIRAC
# from DIRAC import gLogger
# gLogger.setLevel( 'DEBUG' )
#
# DIRAC.gLogger.initialize('test_gLogger','/testSectionDebug')
#
#
# try:
# for i in None:
# pass
# except:
# pass
#
# testList = [{ 'method' : DIRAC.gLogger.... | Andrew-McNab-UK/DIRAC | FrameworkSystem/test/testLogger.py | Python | gpl-3.0 | 1,772 | [
"DIRAC"
] | 4f6481a6a42191c5ce806b9f30b038e38e6cdc05a2b4f1f914d0a94364b71e88 |
#!/usr/bin/env python
"""
Modal analysis of a linear elastic block in 2D or 3D.
The dimension of the problem is determined by the length of the vector
in ``--dims`` option.
Optionally, a mesh file name can be given as a positional argument. In that
case, the mesh generation options are ignored.
The default material ... | BubuLK/sfepy | examples/linear_elasticity/modal_analysis.py | Python | bsd-3-clause | 12,394 | [
"VTK"
] | 29fb0a99d05479f0282f97e5aafc9c82125ec9af43e9238e74fbd42bb652fbd2 |
# ######################################################################
# Copyright (c) 2014, Brookhaven Science Associates, Brookhaven #
# National Laboratory. All rights reserved. #
# #
# Redistribution and use in ... | tacaswell/scikit-beam | skbeam/core/feature.py | Python | bsd-3-clause | 9,620 | [
"Gaussian"
] | 6a482bb79eea39e7507c1ca8561a96236a5a62e6b4be2c5c974bdf26d2dd722c |
"""Processes for testing purposes"""
from pywps.Process import WPSProcess
class NoInputsProcess(WPSProcess):
"""This process has no inputs and no outputs"""
def __init__(self):
WPSProcess.__init__(self, identifier = "noinputsprocess",title="No inputs")
class LiteralProcess(WPSProcess):
"""This pro... | openearth/PyWPS | pywps/processes/tests.py | Python | gpl-2.0 | 6,627 | [
"NetCDF"
] | 9ba909d9d5cc1f1b6ca4e8a4b45f4e6c6e13468a4c43ae373d26b547d4a0830e |
""" An example for using gromacs calculator in ase.
Atom positions are relaxed.
A sample call:
./gromacs_example_mm_relax.py hish_waterbox.gro
"""
from ase.calculators.gromacs import Gromacs
import sys
from ase.io import read
infile_name = sys.argv[1]
CALC_MM_RELAX = Gromacs(
init_structure_file=inf... | grhawk/ASE | tools/doc/ase/calculators/gromacs_example_mm_relax.py | Python | gpl-2.0 | 1,057 | [
"ASE",
"Gromacs"
] | 1b44dbb5417c4ab612d3d01cf8da684116f97e57fcd40bb6cad8aa5469dc005e |
# coding=utf-8
# Copyright 2020 The Real-World RL Suite 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 appl... | google-research/realworldrl_suite | realworldrl_suite/environments/humanoid.py | Python | apache-2.0 | 24,975 | [
"Gaussian"
] | dea2057b1f8cf8eeae7f9fbdc6201cfdd65492c8b0b8163c4ba1bee225cdd904 |
import os
import string
import warnings
import numpy as np
from ..grids import RasterField, StructuredField, UnstructuredField
class Error(Exception):
pass
class DimensionError(Error):
def __init__(self, msg):
self._msg = msg
def __str__(self):
return self._msg
class BadFileFormatEr... | csdms/coupling | pymt/portprinter/utils.py | Python | mit | 8,516 | [
"NetCDF"
] | 6a3126a8b226f3c84c69ab3501b2c3c46bdab40e27379bdc95bcfe22561bf240 |
# -*- coding: utf-8 -*-
"""
Python 2.7
Thomas Dunwell, University of Oxford, 2016.
"""
#This script was used in a paper titled "Novel and divergent genes in the evolution of placental mammals" Dunwell et al., In press
#The final output of this script is a tab delimited text file with row headers for each of t... | DrDunwell/Novel-and-divergent-genes-in-the-evolution-of-placental-mammals | Blast_interaction_mapping.py | Python | lgpl-3.0 | 4,440 | [
"BLAST"
] | 42806c5ed3a158a96e806d8cb1979c171bcacd5540ab600906c1def51878c8bf |
# Orca
#
# Copyright 2010 Joanmarie Diggs, Mesar Hameed.
#
# 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 2.1 of the License, or (at your option) any later version.
#
# ... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/desktop_keyboardmap.py | Python | gpl-3.0 | 6,493 | [
"ORCA"
] | adda493c6f99d62fcf88d69ad0c37c348b7b09dc2d05c99f5a7cb32f39f96ef5 |
import httplib
import re
import warnings
try:
from cStringIO import StringIO
except ImportError:
from StringIO import StringIO
from urllib import addinfourl
from django.core.management import call_command
from django.core.urlresolvers import NoReverseMatch, reverse
try:
from django.conf import settings
e... | playpauseandstop/tddspry | tddspry/django/cases.py | Python | bsd-3-clause | 31,519 | [
"VisIt"
] | ec184195562cc9a69af4a37139f9491dfe2082a7ee1df906a33bf9fcc0b60fb1 |
import sys
import pandas as pd
import subprocess,os
sys.path.append('/home/shangzhong/Codes/Pipeline')
sys.stdout = os.fdopen(sys.stdout.fileno(), 'w', 0) # disable buffer
from Modules.f05_IDConvert import extract_from_gene2ref,mRNA_prIDMap2geneIDMap,uniq1stGene,extractIDFromBlastName,mRNA_prID2geneIDRemote,indexUniqli... | shl198/Pipeline | CHOGeneId2HumanId/IdMappingModule.py | Python | mit | 22,411 | [
"BLAST"
] | 589c94670015676d058f5cf047658a3e141661ae03c206d0939112fba255c0c6 |
import ocl
import pyocl
import camvtk
import time
import vtk
import datetime
import math
if __name__ == "__main__":
print ocl.version()
myscreen = camvtk.VTKScreen()
a=ocl.Point(1,0,0)
myscreen.addActor(camvtk.Point(center=(1,0,0), color=(1,0,1)));
b=ocl.Point(0,1,0)
myscreen.addActo... | JohnyEngine/CNC | opencamlib/scripts/drop-cutter/drop_cutter_tst_4.py | Python | apache-2.0 | 2,371 | [
"VTK"
] | b9dca2235372774f7cc7740181b9af5f8120b2dfd4491aaf8cca49d18e257d27 |
# ######################################################################
# Copyright (c) 2014, Brookhaven Science Associates, Brookhaven #
# National Laboratory. All rights reserved. #
# #
# @author: Li Li (lili@bnl.g... | danielballan/scikit-xray | skbeam/core/fitting/xrf_model.py | Python | bsd-3-clause | 55,678 | [
"Gaussian"
] | 5d636cca3d95ae6092654dec223ca37ab9bf974516bb8ac90c3b123e8ed9dab3 |
from django.db import models
from django.conf import settings
from django.contrib.auth.models import User
from registration.models import RegistrationManager
# import the logging library
import logging
from django.core.exceptions import ObjectDoesNotExist
from visits.models import Visit
# Get an instance of a logger
l... | robjordan/unesco_project | unesco/members/models.py | Python | apache-2.0 | 1,267 | [
"VisIt"
] | 9f6448ff18f828edef5f88ad9ebf8d3fb4ddf37464ab235c199377f55e3106df |
from __future__ import division
import numpy as np
import math
from utils import *
from geom import *
import sampler, ensemble
import scipy.stats as stats
import sys
import random
prior = sys.argv[2]
priorType = sys.argv[3]
name = sys.argv[1]
#priorIncl = np.genfromtxt('chains/incl_'+name)
def getPriors(params):
... | astrolitterbox/SAMI | mcmc.py | Python | gpl-2.0 | 6,182 | [
"Galaxy"
] | f3d89adc26ebc5293438f8fdfd70d5ad8633c2b004034f3ebdf3737d738fbce7 |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.u... | acsis-project/emissions | emissions/python/timeseries_1950-2020/regrid_OC_biomass_emissions_n96e_360d.py | Python | gpl-3.0 | 19,222 | [
"NetCDF"
] | 3590cc10bd9e46f6b22428b0bc81f404325f2f3c71a4ddf7b53d0fc3f0b65b27 |
# Orca
#
# Copyright 2004-2009 Sun Microsystems Inc.
#
# 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 2.1 of the License, or (at your option) any later version.
#
# This... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/apps/Thunderbird/speech_generator.py | Python | gpl-3.0 | 3,991 | [
"ORCA"
] | 949ebf10636674ab2abf70210220d8cbf014ac8c6c892f42a922a1742b4aca39 |
#!/usr/bin/python
import httplib2
import os
import sys
from apiclient.discovery import build
from oauth2client.file import Storage
from oauth2client.client import flow_from_clientsecrets
from oauth2client.tools import run
from optparse import OptionParser
# CLIENT_SECRETS_FILE, name of a file containing the OAuth 2... | lhongskie/yt-samples-python | like_video.py | Python | apache-2.0 | 3,219 | [
"VisIt"
] | 38a4752629f0a1d4d3ce136e25926cea1ef7fb6af407bba208fe0948f4c497a8 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Tim Moore
# Contributors:
#
# MDTraj is free software: you can... | hainm/mdtraj | mdtraj/formats/hoomdxml.py | Python | lgpl-2.1 | 5,450 | [
"HOOMD-blue",
"MDTraj"
] | 211c3ffc1eda46fac77d4e2cef6d54a332283c6680625bfc8befd964c4718c24 |
from PyQt4.QtCore import *
from pyExcelerator import *
from pyExcelerator.Utils import *
from blur.Stone import *
from blur.Classes import *
import re
import sys
from defaultdict import DefaultDict
class Report:
def __init__(self,Name,Title,Function):
self.Name = Name
self.Title = Title
self.Function = Functio... | lordtangent/arsenalsuite | python/blur/reports.py | Python | gpl-2.0 | 41,971 | [
"COLUMBUS"
] | 344e416a7135f361f173cb214b61cacc25e473826d1c976b6ce3c23e77e76dfe |
try:
import cPickle as pickle
except:
import pickle
from hashlib import md5
import time
import functools
import base64
from twisted.internet import reactor
from txweb import logger
CACHE_SET_EVENT = 'cache_set'
CACHE_DELETE_EVENT = 'cache_delete'
CACHE_UPDATE_EVENT = 'cache_update'
class CacheManager(object):
... | talkincode/txweb | txweb/redis_cache.py | Python | mit | 5,714 | [
"VisIt"
] | 512efd54b2779aa2aa1558aca9930ca34b66c09f6e8f1daa956c285013b22ee3 |
#
# Copyright (C) 2017 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 vers... | KonradBreitsprecher/espresso | testsuite/auto_exclusions.py | Python | gpl-3.0 | 2,399 | [
"ESPResSo"
] | 0043e4335dd15a67bb0aea5c60e112a754873777aa53897b59dd4b823c320211 |
# 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)
import inspect
from spack.directives import extends
from spack.package import PackageBase, run_after
class RPackage(Pa... | LLNL/spack | lib/spack/spack/build_systems/r.py | Python | lgpl-2.1 | 2,907 | [
"Bioconductor"
] | 623a57fcb6f07ff30502734df66ac36878542b90b76360a26bfa32d1370f5823 |
#**********************************************
# B I P R O P A G A T I O N
#
# This is Demo App for Bipropagation algorithm
# written in Tensorflow 1.0 by Bojan PLOJ.
# This new algorithm and is much faster,
# much more accurate and much more reliable
# than his predecessor - Backpropagation.
# Learning is d... | BojanPLOJ/Bipropagation | BipropagationXOR1.py | Python | gpl-3.0 | 3,032 | [
"NEURON"
] | 7d97db5942e8cc993a37ca8839f22d114703b558ef4e5e77b8c91c4cab7e0e9b |
import os
import sys
import logging
from pymongo import Connection
import json
import random
from flask import Flask, render_template, jsonify
#from flask.ext.socketio import SocketIO, emit
# Ensure the tracking-level directory is on the path. Then use . package notation and __init__ files.
this_dir = os.path.dirnam... | robrant/compare-baskets | geo_app/server_app.py | Python | mit | 10,137 | [
"Amber"
] | 0f292dab604eb12ac59f0ef076b8e258fe6e0f9bd3faa473be8510cd156b41d7 |
# Copyright (C) 2010, Jesper Friis
# (see accompanying license files for details).
"""Definition of the Spacegroup class.
This module only depends on NumPy and the space group database.
"""
import os
import warnings
import numpy as np
__all__ = ['Spacegroup']
class SpacegroupError(Exception):
"""Base excepti... | slabanja/ase | ase/lattice/spacegroup/spacegroup.py | Python | gpl-2.0 | 24,219 | [
"ASE",
"CRYSTAL"
] | cba585c733baac00ec8088969fd353f20d27bbfebfc78536839495aedb9028b5 |
# -*- coding: utf-8 -*-
# Copyright 2007-2022 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at y... | jat255/hyperspy | hyperspy/_signals/eels.py | Python | gpl-3.0 | 79,228 | [
"Gaussian"
] | bb499814b3dfed50364c77f1058e10307b90a65d8642582e16625e0d0e20cd11 |
import os
import sys
import pymbar
import numpy as np
import pandas as pd
import simtk.openmm.app as app
import simtk.openmm as mm
import simtk.unit as u
import mdtraj as md
import simtk.unit as units
kB = u.BOLTZMANN_CONSTANT_kB * u.AVOGADRO_CONSTANT_NA
def GHMCIntegrator(temperature=298.0*u.kelvin, collision_rate=9... | kyleabeauchamp/DBayes | dbayes/dipoles.py | Python | gpl-2.0 | 16,679 | [
"Gaussian",
"MDTraj",
"OpenMM"
] | fbedae143f5f7818913195665a872cd1a0d5b65b3d2c875d526970c5701affa6 |
# 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 RAromaLight(RPackage):
"""Light-Weight Methods for Normalization and Visualization of Micr... | LLNL/spack | var/spack/repos/builtin/packages/r-aroma-light/package.py | Python | lgpl-2.1 | 1,298 | [
"Bioconductor"
] | 0c5c67fc08fd728a58500ae5b4af5c015825aa2f399185e2a9542b46b0f8d93d |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/chronos/test/bigdl/chronos/autots/deprecated/preprocessing/test_fill.py | Python | apache-2.0 | 2,247 | [
"ORCA"
] | d93856eee8540f9999ea0548d693b94d47d1286b24fec1a39a910f284ab5434f |
""" generate a single-file self-contained version of pytest """
import os
import sys
import pkgutil
import py
import _pytest
def find_toplevel(name):
for syspath in sys.path:
base = py.path.local(syspath)
lib = base/name
if lib.check(dir=1):
return lib
mod = base.join... | takluyver/pytest | _pytest/genscript.py | Python | mit | 4,016 | [
"VisIt"
] | 05052ec5ef34fdb199a53f196b710ceae6739902e2a06a1c4b1570f1f9c2f4e2 |
"""
@name: PyHouse/src/Modules/_test/test_Hvac.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2017 by D. Brian Kimmel
@license: MIT License
@note: Created on Jul 31, 2015
@Summary:
"""
from twisted.trial import unittest, reporter, runner
from Modules.Housing.Hvac ... | DBrianKimmel/PyHouse | Project/src/Modules/House/_test/test_Hvac.py | Python | mit | 717 | [
"Brian"
] | 39e4563f25d32021d3a19dadea02494c96c4cf782e75ba747595f95ebc2ecf13 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2020, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Parser for GAMESS(US) output files"""
import re
import numpy
from cclib.parser import logfileparser
from cclib.par... | cclib/cclib | cclib/parser/gamessparser.py | Python | bsd-3-clause | 74,137 | [
"Firefly",
"GAMESS",
"Gaussian",
"cclib"
] | ae59f4d296fadba35fd820d169728dd03fb8f154abe9f7745bb09c847927e00c |
#!/usr/bin/env python
# Euler tilting angles extraction reverse test
# First, distort on the known angle, then extract tilting and check if it is the same
# Author: Evgeny Blokhin
import math
import random
import unittest
import six
from numpy import array
import set_path
from tilde.core.settings import settings
fr... | ansobolev/tilde | tests/apps/perovskite_tilting/tilt_reverse.py | Python | mit | 3,328 | [
"ASE",
"CRYSTAL"
] | 5575b82ad2806a970d09154d343424a5bc2d7608217856d9ce6197fa17f37e27 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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
#... | dgasmith/psi4 | psi4/driver/p4util/spectrum.py | Python | lgpl-3.0 | 13,864 | [
"Avogadro",
"Gaussian",
"Psi4"
] | 2e72864c6f5b2058908badbc8fc85b743ecdb786ddb02c0f0e8f9b8f26db1246 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2010 Nick Hall
# Copyright (C) 2011 Tim G L Lyons
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of t... | prculley/gramps | gramps/gui/displaystate.py | Python | gpl-2.0 | 22,278 | [
"Brian"
] | d30eec61f9c9d204b41c7bc7d059ca30c9ab4d1acb5e5f890bf45beb57bff1e3 |
# -*- coding: utf-8 -*-
#
# furl - URL manipulation made simple.
#
# Arthur Grunseid
# grunseid.com
# grunseid@gmail.com
#
# License: Build Amazing Things (Unlicense)
import sys
import warnings
from abc import ABCMeta, abstractmethod
import six
from six.moves import urllib
import furl
from furl.omdict1D import omdi... | penyatree/furl | tests/test_furl.py | Python | unlicense | 75,238 | [
"BLAST"
] | 70d99ab82034551b6337a7a47428f19f62d26b634b30ed735c4f17fbd4eb46cd |
import ocl
import camvtk
import time
import vtk
import datetime
import math
def drawLoops(myscreen, loops, loopcolor):
nloop = 0
for lop in loops:
n = 0
N = len(lop)
first_point=ocl.Point(-1,-1,5)
previous=ocl.Point(-1,-1,5)
for p in lop:
if n==0: # don't dra... | JohnyEngine/CNC | opencamlib/scripts/waterline/waterline_5_30ball.py | Python | apache-2.0 | 2,795 | [
"VTK"
] | 1a4b17272f0c106eb5a4a3f63746443816a55f470b662011c6f15e6e46dcaf7d |
# -*- coding: utf-8 -*-
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import numpy as np
import abel
import os
from glob import glob
import scipy
from scipy.special import eval_legendre
from scipy import ndimage
###... | PyAbel/PyAbel | abel/linbasex.py | Python | mit | 20,441 | [
"Gaussian"
] | f1b5771c664795d95aa922abf8fdecddac71f05f3fcb9570d7eefc5d9e6846ae |
# This file is part of kernelconfig.
# -*- coding: utf-8 -*-
import abc
import collections.abc
import operator
from . import symbol
from .solcache import SolutionCache, merge_solutions
__all__ = [
"clear_cache",
"merge_solutions",
"Expr",
"Expr_And",
"Expr_Not",
"Expr_Or",
"Expr_Constant... | dywisor/kernelconfig | kernelconfig/kconfig/symbolexpr.py | Python | gpl-2.0 | 37,895 | [
"VisIt"
] | 33e3c941ff57433d0d2d00ecf06ec1726383d0b46d88d7e15647303ee6ebcbc5 |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.u... | acsis-project/emissions | emissions/python/timeseries_1960-2020/regrid_nC4H10_emissions_n96e_greg.py | Python | gpl-3.0 | 18,833 | [
"NetCDF"
] | 501ab3f11737554f62ee659b887ec18d8929d8af309b70d8788ca1aa1fa5f7c2 |
#!/usr/bin/env python
# coding: UTF-8
#
## @package treeGL
#
# A tree exhibitor based on OpenGL.
# Non-commercial use only.
#
# Fedora:
# - sudo dnf install python2-pyopengl or python3-pyopengl
#
# Ubuntu:
# - sudo apt-get install python2-opengl or python3-opengl
#
# MacOS:
# - sudo port install py27-opengl ... | spidey/academic-works | bstset/src/treeGL.py | Python | gpl-3.0 | 23,274 | [
"VisIt"
] | 75c27d43cc1f1b0c128a7d66bed0d199c95619513ec1ab4783dc5f85cd322ed3 |
from scipy import signal
import numpy as np
import matplotlib
matplotlib.use("TkAgg")
import matplotlib.pyplot as plt
from scipy.fftpack import fft,ifft,fftshift
import math
import random
import cmath
import test_signals
def plot_fft(samplesa, rate):
fft_samps=fft(samplesa)
T= 1.0 /float(rate)
num_samps=le... | SuperDARNCanada/borealis | tools/testing_utils/filter_testing/frerking/decimator.py | Python | gpl-3.0 | 6,529 | [
"Gaussian"
] | c6f6615e69a7be0e479782099542762051ce22e8eb6066b770f32dd1b082a62a |
# -*- coding: utf-8 -*-
#
# test_rate_neuron_communication.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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... | sdiazpier/nest-simulator | testsuite/pytests/test_rate_neuron_communication.py | Python | gpl-2.0 | 9,860 | [
"NEURON"
] | 8a7eb665d43be9a7da1598b472bba3f1a0db76940ba48716fac14a0d88713686 |
from collections import defaultdict
import shutil
import sys
from defaults import *
from vcf_utils import *
from sv_interval import SVInterval, get_gaps_file, interval_overlaps_interval_list, merge_intervals, merge_intervals_recursively
from pindel_reader import PindelReader
from breakdancer_reader import BreakDancerR... | msahraeian/metasv | metasv/main.py | Python | bsd-2-clause | 17,480 | [
"pysam"
] | bef53fb1f68cb49cb8fcf4df87f2189ec8c02b3ad7145f9ad9f68008c9a4ff99 |
"""
Copyright (C) 2004-2015 Pivotal Software, Inc. All rights reserved.
This program and the accompanying materials are made available under
the terms of the 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
... | rvs/gpdb | src/test/tinc/tinctest/models/concurrency/test/test_concurrency_test_case.py | Python | apache-2.0 | 4,095 | [
"ORCA"
] | 3fedd3207d40d2b3eaeaf0b545de0852e86ba0f60b71752227f00b209b72b1b5 |
""" TaskManager contains WorkflowTasks and RequestTasks modules, for managing jobs and requests tasks
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
# pylint: disable=protected-access
import six
import time
from six import StringIO... | yujikato/DIRAC | src/DIRAC/TransformationSystem/Client/TaskManager.py | Python | gpl-3.0 | 42,216 | [
"DIRAC"
] | 1852779be54c79f1f1b1aa4ea9e3ad807e61471d7b34bfb1cd5e41ca5f8adfcf |
#!/usr/bin/env python
# This example demonstrates how to use a constraint polygon in
# Delaunay triangulation.
import vtk
from vtk.util.colors import peacock
# Generate the input points and constrained edges/polygons.
points = vtk.vtkPoints()
points.InsertPoint(0, 1, 4, 0)
points.InsertPoint(1, 3, 4, 0)
points.Inser... | CMUSV-VisTrails/WorkflowRecommendation | examples/vtk_examples/Modelling/constrainedDelaunay.py | Python | bsd-3-clause | 4,503 | [
"VTK"
] | b1d8cc0e215b14259111df14c97331406a0f89e9a0de41947b85918b38151733 |
# Copyright 2009 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | tallstreet/jaikuenginepatch | common/im.py | Python | apache-2.0 | 12,036 | [
"VisIt"
] | 6d92b36764ebc9dbe32414b319f4b441d66a6448243f1dfb430bb123bd5e6e7f |
#!/usr/bin/env python
# This example shows how to use a transparent texture map to perform
# thresholding. The key is the vtkThresholdTextureCoords filter which
# creates texture coordinates based on a threshold value. These
# texture coordinates are used in conjuntion with a texture map with
# varying opacity and int... | VisTrails/VisTrails | examples/vtk_examples/VisualizationAlgorithms/TextureThreshold.py | Python | bsd-3-clause | 4,832 | [
"VTK"
] | 366c01d7f216d652a45e48d3b66c9345776385461d97ed24092250ed1aa246fc |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | lgarren/spack | var/spack/repos/builtin/packages/plumed/package.py | Python | lgpl-2.1 | 7,198 | [
"Amber",
"ESPResSo"
] | 014ac8c11f4d862ac6cdb6e3c769c445d2141f4a0983a0824c82bea21dbe1db7 |
# coding: utf-8
from __future__ import division, unicode_literals, print_function
"""
Classes for reading/manipulating/writing VASP ouput files.
"""
__author__ = "Shyue Ping Ong, Geoffroy Hautier, Rickard Armiento, " + \
"Vincent L Chevrier, Ioannis Petousis, Stephen Dacek"
__credits__ = "Anubhav Jain"
__copyri... | Dioptas/pymatgen | pymatgen/io/vaspio/vasp_output.py | Python | mit | 93,126 | [
"CRYSTAL",
"VASP",
"pymatgen"
] | b171e4c890e9a5ee83a500f563fa6a1cb5b15ce1ebee7dceb4796ccb1ceeffdf |
#!/usr/bin/env python
#
# Electrum - lightweight Bitcoin client
# Copyright (C) 2015 Thomas Voegtlin
#
# 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 y... | vcoin-project/electrum | plugins/__init__.py | Python | gpl-3.0 | 4,981 | [
"VisIt"
] | ef0e6ad36b8678ea71e0ef82b7e3a6bba450f681afb017727277f96c2316b93b |
# -*- coding: utf-8 -*-
""" ymir._ansible
Defines a ansible mixin for the base ymir service service class
"""
import os
import json
from fabric import api
from fabric.colors import yellow
from peak.util.imports import lazyModule
from ymir import util
from ymir import data as ydata
yapi = lazyModule('ymir.api')
... | mattvonrocketstein/ymir | ymir/mixins/_ansible.py | Python | mit | 7,060 | [
"Galaxy"
] | 266dada7add90ca099fb761acd0cd4f46dddcf5512b38783ac53d1ab2b6a6b04 |
"""Biot problem with the no-penetration BC on the Walls boundary region."""
# c: 10.03.2009
import os
import numpy as nm
from sfepy.mechanics.matcoefs import stiffness_tensor_lame
def define():
from sfepy import data_dir
filename = data_dir + '/meshes/3d/cylinder.mesh'
output_dir = 'output'
return def... | olivierverdier/sfepy | examples/biot/biot_npbc.py | Python | bsd-3-clause | 5,614 | [
"VTK"
] | 5f25e94583ac8a32fac56b51a3d8efad3508e555cd9f0382d67841b06e372e35 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/datastores/base.py | Python | gpl-3.0 | 3,538 | [
"Brian"
] | e9271616cab0b88ac7b8c24cea84a72eb931a20913ca1e17e2713d5237ba1693 |
# This code is so you can run the samples without installing the package
import sys
import os
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
#
testinfo = "f 10 0.033, s, f 20 0.033, s, f 30 0.033, s, f 30 0.033, s, q"
tags = "particles, Meteor"
import pyglet
import cocos
from cocos.director import ... | eevee/cocos2d-mirror | test/test_particle_meteor.py | Python | bsd-3-clause | 911 | [
"Galaxy"
] | 119461431a9b01a8f0cdca4ff53561fd3e5f776e723ddb1c870d5b8e8326ebe7 |
# coding: utf-8
# # Profile Classification Model with python
# ## Classic workflow demonstration
# Created on Sat Feb 4 08:32:46 2017
#
# We're going to classify Argo data with the following workflow:
# - Load netcdf Argo profiles on Standard Depth Levels
# - Normalize profiles
# - Compress the collection with PC... | obidam/pcm | python/PCM-workflow-classic-demo.py | Python | gpl-3.0 | 20,582 | [
"NetCDF"
] | 3f598673686bc3b91b92056a38598d0af66c4cb4b3f8fd89370861f8d0bcb66c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function
import os
import shutil
import time
import subprocess
import numpy as np
from .phonopy_conf_creator import PhonopyConfCreator
from vasp.poscar import Poscar
from autotools import symlink_force
class PhononCalculator(object):
def _... | yuzie007/ph_analysis | ph_analysis/phonon_calculator.py | Python | mit | 6,728 | [
"VASP",
"phonopy"
] | 1f2e55f42e96de7116bd62a16e6944cab4338847094bb65d1ff5258e15fe8257 |
#!/usr/bin/env python
########################################################################
#
# (C) 2015, Chris Houseknecht <chouse@ansible.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... | alexanderturner/ansible | lib/ansible/galaxy/login.py | Python | gpl-3.0 | 4,511 | [
"Galaxy"
] | 8a8c7ae6f65331c0e53003f6edfab17f21070bdf3c4e5e16904ff8882463179b |
#! python3
# randomQuizGenerator.py - Creates quizzes with questions and answers in
# random order, along with the anwser key.
import random
# The quiz data. Keys are states and values are their capitals.
capitals = {'Alabama': 'Montgomery', 'Alaska': 'Juneau', 'Arizona': 'Phoenix',
'Arkansas': 'Little Roc... | WaR1o/SimpleScripts | randomQuizGen/randomQuizGenerator.py | Python | gpl-3.0 | 3,118 | [
"COLUMBUS"
] | 5f4a69554167bcbad05443fa1be25cde7d55731c35b42323d13f1e881b01c426 |
#!/usr/bin/python
# Emacs settings: -*- tab-width: 4 -*-
#
# Copyright (c) 2002-2003 Apple Computer, Inc. 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://... | jxfengzi/MdnsdTest | mdnsresponder/mDNSPosix/parselog.py | Python | mit | 10,080 | [
"Jaguar"
] | 5327be264a800feadc18420e46786ddeeb738e5095634552a69f109dd532055a |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | annarev/tensorflow | tensorflow/python/kernel_tests/signal/spectral_ops_test.py | Python | apache-2.0 | 15,750 | [
"Gaussian"
] | 98bcade31657ffdb48a66f70777b49a9901d40602dfe79fc5e104c66d2415d31 |
"""
Example of contour plotting with pyvisi - vtk specific code
"""
# set up some data to plot
from numpy import *
# the x and y axes
x = arange(-2,2,0.2, dtype=floating)
y = arange(-2,3,0.2, dtype=floating)
# pick some interesting function to generate the data in the third dimension
# this is the one used in the m... | paultcochrane/pyvisi | examples/renderers/vtk/contourPlot.py | Python | gpl-2.0 | 4,187 | [
"VTK"
] | 23ec972da3f375b5a015980921c8cd429c764551777a11abeae46eb47da5d271 |
from django.conf.urls import patterns, url
from django.contrib.auth.decorators import login_required
from django.views.generic import TemplateView
from catmaid.views import CatmaidView, ExportWidgetView
# A regular expression matching floating point and integer numbers
num = r'[-+]?[0-9]*\.?[0-9]+'
integer = r'[-+]?[... | fzadow/CATMAID | django/applications/catmaid/urls.py | Python | agpl-3.0 | 22,509 | [
"NEURON"
] | 71e4604b45e5a36f0a530aba279ea772b4d336a0284cf845c4031861099e12f4 |
#!/usr/bin/env python
"check build configuration"
#
# Copyright (C) 2010-2017 ABINIT Group (Yann Pouillon)
#
# This file is part of the ABINIT software package. For license information,
# please see the COPYING file in the top-level directory of the ABINIT source
# distribution.
#
# FIXME: detect duplicate definitions
... | jmbeuken/abinit | abichecks/scripts/check-build-config.py | Python | gpl-3.0 | 6,607 | [
"ABINIT"
] | 2ca5e476e4ac5ee7869c25f0750ffefd09d8aa6b6f0e41d9fbd0de21f515ade9 |
""" Used by the executors for dispatching events (IIUC)
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import threading
import time
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.Core.Utilities.ReturnValues import isReturnStructure
from DIRAC.Core... | ic-hep/DIRAC | src/DIRAC/Core/Utilities/ExecutorDispatcher.py | Python | gpl-3.0 | 31,814 | [
"DIRAC"
] | b3c26b53ebddb9bbdebd41facac8ef31f8ea8fb4da9e5bbce6f779456b2c82d5 |
#########################################################################
#
## This program is part of 'MOOSE', the
## Messaging Object Oriented Simulation Environment.
## Copyright (C) 2013 Upinder S. Bhalla. and NCBS
## It is made available under the terms of the
## GNU Lesser General Public License version... | dilawar/moose-full | moose-examples/snippets/crossComptNeuroMesh.py | Python | gpl-2.0 | 8,625 | [
"MOOSE",
"NEURON"
] | 8c0d5906ac029ada8006b111e777cebec206a997a39faac1e995351350fd5f3a |
"""A collection of non-environment specific tools"""
import sys
import os
from robofab.objects.objectsRF import RInfo
if sys.platform == "darwin" and sys.version_info[:3] == (2, 2, 0):
# the Mac support of Jaguar's Python 2.2 is broken
have_broken_macsupport = 1
else:
have_broken_macsupport = 0
def readGlyphCon... | adrientetar/robofab | Lib/robofab/tools/toolsAll.py | Python | bsd-3-clause | 3,934 | [
"Jaguar"
] | 064cfc26b29b1393d20464acad4ea3014b32e477c03abeaf4778a52a59f95031 |
##########################################################################
#
# Copyright 2008-2010 VMware, Inc.
# All Rights Reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software withou... | xranby/apitrace | gltrace.py | Python | mit | 40,239 | [
"VisIt"
] | 4f5a73bc47b6df13d6da34aa29feac42ca0b5f9a853265217393404b4205fb29 |
# -- TRAINING for full [200, 400] window
from keras.layers import containers
from keras.models import Sequential
from keras.layers.core import Dense, Dropout, AutoEncoder, MaxoutDense, Activation, Merge
from keras.layers.advanced_activations import PReLU
from keras.layers.embeddings import Embedding
from keras.layers.n... | ml-slac/deep-jets | s-to-b-training.py | Python | mit | 10,171 | [
"Gaussian"
] | e31796d4fd24618d4b01afc884c97c3fce9f5ff64959048355b30a8b8c4cc14f |
from __future__ import print_function, division, unicode_literals
import copy
import numpy as np
import math
import itertools
from collections import Counter
from sympy import Point3D, Plane,Line3D
from operator import itemgetter
from pymatgen import Structure, Element, Composition
from pymatgen.analysis.structure... | henniggroup/MPInterfaces | mpinterfaces/mat2d/preparation.py | Python | mit | 64,013 | [
"CRYSTAL",
"pymatgen"
] | daaa64a921d52775114349b30be2bbaea6940f49b4f650b789219a5cb49d288b |
"""Tests for the DIRAC.Core.Utilities.Extensions module"""
import DIRAC
from DIRAC.Core.Utilities.Extensions import (
findSystems,
findAgents,
findExecutors,
findServices,
findDatabases,
extensionsByPriority,
getExtensionMetadata,
)
def test_findSystems():
systems = findSystems([DIRAC]... | DIRACGrid/DIRAC | src/DIRAC/Core/Utilities/test/Test_Extensions.py | Python | gpl-3.0 | 1,052 | [
"DIRAC"
] | 2ca5f9b17f61d47a5db313e130ca9b44f4d6498f583f8f529ff36d1e4af2a061 |
#!/usr/bin/python
"""
A module with operations useful for Kalman filtering.
"""
import numpy as np
import math
import scipy.linalg
from builtins import range
l2pi = math.log(2 * math.pi)
def lognormpdf(err, S):
"""
Calculate gaussian probability density of err, when err ~ N(0,sigma)
"""
tmp = err.re... | jerkern/pyParticleEst | pyparticleest/utils/kalman.py | Python | lgpl-3.0 | 7,181 | [
"Gaussian"
] | 4b94f61367b886977992146f142b12b392764a3bf711a6c03435936d3617a5b3 |
import vcr
import pytest
from scrapi.base import helpers
class TestHelpers(object):
def test_format_one_tag(self):
single_tag = ' A single tag '
single_output = helpers.format_tags(single_tag)
assert single_output == ['a single tag']
assert isinstance(single_output, list)
de... | jeffreyliu3230/scrapi | tests/test_helpers.py | Python | apache-2.0 | 3,167 | [
"CRYSTAL"
] | f21c6b69a0761fbefda9f9eebff6eca95eb3c476a2c639107583e40356534470 |
# Write the benchmarking functions here.
# See "Writing benchmarks" in the asv docs for more information.
import os
import sys
import py_entitymatching as mg
p = mg.get_install_path()
datasets_path = os.sep.join([p, 'datasets', 'example_datasets'])
ob = mg.OverlapBlocker()
c... | anhaidgroup/py_entitymatching | benchmarks/benchmark_overlap_blocker.py | Python | bsd-3-clause | 11,060 | [
"VisIt"
] | 783a15cdcfc68330f4ce12eff3ada012e1dd0b34bffa11cfaf3678b46e2eae1e |
import re
from Bio import pairwise2
from Bio.Seq import Seq
from collections import defaultdict
from mirtop.mirna.mintplates import convert
import mirtop.libs.logger as mylog
logger = mylog.getLogger(__name__)
class hits:
""""Class with alignment information."""
def __init__(self):
self.sequence = ... | miRTop/mirtop | mirtop/mirna/realign.py | Python | mit | 16,215 | [
"Biopython"
] | 9cab972426209c1f365d15912d1082d4b5e7df05e4cff8b6e6d945075840fc0b |
#!/usr/bin/env python
"""
Dispersion analysis of a heterogeneous finite scale periodic cell.
The periodic cell mesh has to contain two subdomains Y1 (with the cell ids 1),
Y2 (with the cell ids 2), so that different material properties can be defined
in each of the subdomains (see ``--pars`` option). The command line ... | vlukes/sfepy | examples/linear_elasticity/dispersion_analysis.py | Python | bsd-3-clause | 35,004 | [
"VTK"
] | e455627e5e0a14fd63464672a499496171d0ed02c26aa027fd2b5187ca458f71 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | wdwvt1/scikit-bio | skbio/stats/ordination/_base.py | Python | bsd-3-clause | 16,284 | [
"scikit-bio"
] | 5d13f048b15c6ab33d45ba409c5c1d37d29b009a7f138a8ce8409b583c37b399 |
#!/usr/bin/env python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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 redistri... | dgasmith/psi4 | psi4/share/psi4/fsapt/fsaptdiff.py | Python | lgpl-3.0 | 4,127 | [
"Psi4"
] | 1a62d3236a5d0ab477e8cf20588d14dcfed88ef5d30a5cb64906108709ca750a |
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