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##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/r-rtracklayer/package.py | Python | lgpl-2.1 | 2,610 | [
"Bioconductor"
] | ffb1c635e0ff41956c824b5ec3ad0cacb902857e172341aef081f59b3341b124 |
#!/usr/bin/env python
import sys
from os import path
import os
import argparse
import urllib.request
from types import ModuleType
from collections import OrderedDict
from inspect import cleandoc
import ast
from codegen import SourceGenerator
from lxml import html
from slugify import slugify
import html2text
HTMLCONVER... | denz/ldp | test/requirements/w3tests_update.py | Python | bsd-3-clause | 9,216 | [
"VisIt"
] | 9e6510312ef11493f86b3069af91a2947239b9353f6a749e3b1897688f330ff2 |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/m_init_dens_libnao.py | Python | apache-2.0 | 991 | [
"PySCF"
] | 378b443a79dc089dba55f996d7512eadb6c834822de17cf97233a00248861b30 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
urlpatterns = [
url(r'^$', TemplateView.as_view(templ... | joanneko/goodbooks | config/urls.py | Python | bsd-3-clause | 2,273 | [
"VisIt"
] | f65cdff8a5bebf82380ce62e2a330ddf079e086647b21b3c463c3d2175b5818d |
""" Module holding function(s) creating the pilot wrapper.
This is a DIRAC-free module, so it could possibly be used also outside of DIRAC installations.
The main client of this module is the SiteDirector, that invokes the functions here more or less like this::
pilotFilesCompressedEncodedDict = getP... | fstagni/DIRAC | WorkloadManagementSystem/Utilities/PilotWrapper.py | Python | gpl-3.0 | 8,620 | [
"DIRAC"
] | dcf60c3f00b6bc0f6e92d6dc08e430fbe17b575ef3a84cce56bd88ee69000306 |
#
# 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/orca/test/bigdl/orca/learn/spark/test_estimator_for_spark.py | Python | apache-2.0 | 26,014 | [
"ORCA"
] | 16f8c5af440a797117156e94da8dd8c01977decfa4c286e12250e586bca9683e |
import unittest
import copy
import sys
from nose.tools import assert_true
import numpy as np
from numpy.testing import (assert_array_equal, assert_array_almost_equal,
assert_raises)
from scipy import stats
from sklearn import mixture
from sklearn.datasets.samples_generator import make_spd_ma... | valexandersaulys/airbnb_kaggle_contest | venv/lib/python3.4/site-packages/sklearn/mixture/tests/test_gmm.py | Python | gpl-2.0 | 17,414 | [
"Gaussian"
] | affaa24724c36f637864b98d192e29dd25f1794b4678017a0f0381c5c8ddd168 |
#!/home/GLBRCORG/mplace/anaconda3/bin/python
"""
Program: MotifxPreAlign.py
Purpose: Use a list of phosphorylated peptide information to create a pre-aligned
peptide file for the motifx website.
Program is called from Motifx.py, but can also be run standalone from
the command line, outp... | mmacgilvray18/Phospho_Network | MotifxPreAlign.py | Python | gpl-3.0 | 13,261 | [
"Biopython"
] | 0a537a7844c3701ed37e97f1bdbcae9936180307b77418321f3a05bb5e698531 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Makes sure that all files contain proper licensing information."""
import json
import optparse
import os.path
import subproces... | M4sse/chromium.src | tools/checklicenses/checklicenses.py | Python | bsd-3-clause | 16,482 | [
"Galaxy"
] | 2534eb56fe3ba8067b1a6811a35f64503344f8ddb692099e8a742eada4a6ae3e |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from py.path import local
import os
class ClassRegistry(dict):
"hold and register classes by nickname, to select later"
def register(self, name):
def inner(cls):
self[name] = cls
return cls
return inner
def files_in_dir(tar... | BrianHicks/perch | perch/utils.py | Python | bsd-3-clause | 414 | [
"VisIt"
] | 8925af4f5dc0c327cd9a7bb757e4fab6222a1e1461943a45a0ebd3012b1cf711 |
# -*- coding: utf-8 -*-
#coding=utf-8
import sys,os
reload(sys)
sys.setdefaultencoding('utf8')
import logging
import urllib
import hashlib
import socket
import urllib2
from suds.client import Client
import xmltodict
from datetime import datetime
from collections import defaultdict
from lxml import html
import base... | XiaodunServerGroup/xiaodun-platform | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 50,293 | [
"VisIt"
] | af92c62ad7e9e1730d1ed6a06b8ed9a39d8140e8d240a9f1537ac8fd1a9d24a1 |
import peel
import pymolecule
#import numpy
my_params = peel.defaultParams
my_protein = pymolecule.Molecule()
my_protein.fileio.load_pdb_into('2gfc_reduced.pdb', serial_reindex=True, resseq_reindex=False)
my_peel = peel.peel(my_protein, my_params)
my_peel.write_vmd_script('visualize_2gfc.vmd', peel.defaultParams)
#po... | j-wags/POVME | binana/tests/peel_2gfc_basic/2gfcTest.py | Python | gpl-3.0 | 1,236 | [
"VMD"
] | ace9a9cf2f61e28d75a7b5b4b078d72868b88706001036405225d5e479af478a |
#
# 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... | Acehaidrey/incubator-airflow | airflow/utils/log/logging_mixin.py | Python | apache-2.0 | 6,009 | [
"Elk"
] | 6c0367a1b8d051aa38d6d010833f539a8b02ba73e0de6fbb469f70c1bf68b1c0 |
#!/usr/bin/python
# =============================================================================================
# COPYRIGHT NOTICE
#
# Written by Michael R. Shirts <mrshirts@gmail.com>.
#
# Copyright (c) 2012 The University of Virginia. All Rights Reserved.
#
# This program is free software; you can redistribute it ... | shirtsgroup/checkensemble | checkensemble/checkensemble.py | Python | gpl-2.0 | 50,763 | [
"Gromacs"
] | 24ebca8109c6abc26bc704ea03c3a29633e017abb0573cef61971761f9b7a4a9 |
from .schemas import (
schema_absorption_spectrum, schema_derivative_couplings,
schema_distribute_absorption_spectrum, schema_distribute_derivative_couplings,
schema_distribute_single_points, schema_cp2k_general_settings, schema_single_points)
from .templates import (create_settings_from_template, valence_e... | felipeZ/nonAdiabaticCoupling | nac/workflows/input_validation.py | Python | mit | 8,570 | [
"CP2K"
] | c6d19e6530b052127c35110ed882e2eb9aa743a387ec012f1a2a9d6483fa1dbf |
# -*- coding: utf-8 -*-
"""Tests for the umbrella node-link JSON exporter."""
import unittest
from pybel.io.umbrella_nodelink import to_umbrella_nodelink
from tests.test_io.test_cx.examples import example_graph
class TestUmbrellaNodeLinkExporter(unittest.TestCase):
"""Tests for the umbrella node-link JSON expo... | pybel/pybel | tests/test_io/test_umbrella_nodelink.py | Python | mit | 1,868 | [
"Pybel"
] | 800796712ed0b1cb63e382810d5ba3c17d0ec1c4864df89c80a7bbfb0969ef85 |
#!/usr/bin/env python
#Schedule is Call, Long, Short, MVSC, Vacation, Regina
#1:'Jason', 2:'Brian', 3:'Dick', 4:'Mark', 5:'Tim', 6:'Ryan'
import numpy as np
import itertools
import random
import sys
import math
import logging
import two_opt
from cost import cost
def gen_permutations(n, mvsc_list, regina_list): #Gene... | jbolinge/scheduler | sim_anneal.py | Python | lgpl-3.0 | 4,665 | [
"Brian"
] | 722df513c53b4bdfd245d03a9b444728e690b515e1359e3f0d9cc30aa89f1b6e |
"""An implementation of the Zephyr Abstract Syntax Definition Language.
See http://asdl.sourceforge.net/ and
http://www.cs.princeton.edu/research/techreps/TR-554-97
Only supports top level module decl, not view. I'm guessing that view
is intended to support the browser and I'm not interested in the
browser.
... | google/google-ctf | third_party/edk2/AppPkg/Applications/Python/Python-2.7.2/Parser/asdl.py | Python | apache-2.0 | 11,733 | [
"VisIt"
] | 63bb05dee87dc3b96b5017a78c808a2f286920327c855c6692c89f4f2bdeae56 |
#!/usr/bin/python
########################################################################
# 27 April 2015
# Patrick Lombard, Centre for Stem Stem Research
# Core Bioinformatics Group
# University of Cambridge
# All right reserved.
########################################################################
import subpro... | pdl30/pyatactools | pyatactools/atac_norm.py | Python | gpl-2.0 | 8,449 | [
"HTSeq"
] | bc67a0ae1ce1c10ace085fefbb8e345bedd4a2cb2f43462cc2f0e3544a3cce32 |
import re
import mdtraj
from mdtraj.testing.docstrings import docstring_verifiers
from mdtraj.testing.docstrings import import_all_modules
SKIP_MODULES = [
'mdtraj\.utils\.external',
'mdtraj\.utils\.six',
'mdtraj\.utils\.unit\.unit_math',
'mdtraj\.utils\.unit\.baseunit',
'mdtraj\.utils\.unit\.prefi... | casawa/mdtraj | mdtraj/tests/test_docstrings.py | Python | lgpl-2.1 | 937 | [
"MDTraj"
] | 0014e13cbda8b8d0625cba5991a43888d4f16d075df0d3b32153e66263ecdb0d |
'''
Defines the main analysis functions which are called by the
PyGeoNS executable.
'''
from __future__ import division
import numpy as np
import logging
import subprocess as sp
from pygeons.main.fit import fit
from pygeons.main.reml import reml
from pygeons.main.strain import strain
from pygeons.main.autoclean impor... | treverhines/PyGeoNS | pygeons/main/main.py | Python | mit | 24,474 | [
"Gaussian"
] | 69398f889b6a74f739d022e2d2eb448231b46b41837bff7d865918bf5f9c1dba |
# module based on EGADS/netcdf_io.py created by Matt Freer in the EUFAR framework
import netCDF4
class FileCore(object):
def __init__(self, filename=None, perms='r', **kwargs):
self.f = None
self.filename = filename
self.perms = perms
for key, val in iter(kwargs.items()):
... | eufarn7sp/asmm-eufar | functions/netcdf_lite.py | Python | bsd-3-clause | 3,788 | [
"NetCDF"
] | 728ed1591895b0238aaa3b9eeaec0e773a323f0ad3a93302f9a9ce3d645acce6 |
# coding: utf-8
#
# drums-backend a simple interactive audio sampler that plays vorbis samples
# Copyright (C) 2009 C.D. Immanuel Albrecht
#
# 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 Fou... | immo/pyTOM | df/df_experimental.py | Python | gpl-3.0 | 7,868 | [
"NEURON"
] | 2a5b8db4673ae754ea16ae5b87867d26d9aef6a210ce567ebfb590e98113f09d |
import os
import time
from core.data.data_migrations import insert_all_permissions
from django.conf import settings
from django.contrib.staticfiles.testing import StaticLiveServerTestCase
from selenium import webdriver
from selenium.webdriver.support.ui import WebDriverWait, Select
from selenium.common.exceptions impo... | agripo/website | functional_tests/base.py | Python | gpl-2.0 | 12,329 | [
"VisIt"
] | ff3a755d524f8154f55d555f22ecd8ee234c42ae05e420423880da4b2654d73c |
from astropy.io import fits
from astropy import units as u
import numpy as np
from astropy import constants
from FITS_tools import cube_regrid
def extract_subcube(cubefilename, outfilename, linefreq=218.22219*u.GHz,
debug=False, smooth=False, vsmooth=False):
ffile = fits.open(cubefilename)
... | keflavich/apex_otf_tools | apex_otf_tools/extract_subcube.py | Python | bsd-3-clause | 2,814 | [
"CDK"
] | c8cb359ff3bda6a511400cd89a03e0fda66a1cf271867bcd3dcadf26e46f6666 |
###### WELCOME THIS IS THE SOURCE CODE OF Snakez ########
print( "\033[1;34m _____ __" )
print( " / ___/____ ____ _/ /_____ ____")
print( " \__ \/ __ \/ __ `/ //_/ _ \/_ / ")
print( " ___/ / / / / /_/ / ,< / __/ / /_ ")
print("/____/_/ /_/\__,_/_/|_|\___/ /___/ FRAMEWORK CREATED BY : \... | splinterk/snakez | snakez.py | Python | gpl-3.0 | 876 | [
"VisIt"
] | a0421db123c99fd1cf93ff7472bfb2bc8875061326a7f6c126c2045e60571a73 |
"""
DIRAC.StorageManagementSystem.Service package
"""
| DIRACGrid/DIRAC | src/DIRAC/StorageManagementSystem/Service/__init__.py | Python | gpl-3.0 | 57 | [
"DIRAC"
] | 6e0d0d94d9ce0a759eea763fa33c668d1b77492b04690788b2f1d88e64badb6f |
"""
[8/22/2012] Challenge #90 [difficult] (Alien P=NP reductions)
https://www.reddit.com/r/dailyprogrammer/comments/ynw9q/8222012_challenge_90_difficult_alien_pnp/
Ancient aliens have come down from earth and announced that, clearly, P=NP, and they've been trying to explain it to us
for years. Something about it bei... | DayGitH/Python-Challenges | DailyProgrammer/DP20120822C.py | Python | mit | 1,417 | [
"CRYSTAL"
] | 926219bd00aa1d75e2055a54f4f3008925189ab35883c99da342ac955894a06c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# Copyright (C) 2013 Radim Rehurek <me@radimrehurek.com>
# Licensed under the GNU LGPL v2.1 - http://www.gnu.org/licenses/lgpl.html
"""
Produce word vectors with deep learning via word2vec's "skip-gram and CBOW models", using either
hierarchical softmax or negative samp... | duyet-website/api.duyet.net | lib/gensim/models/word2vec.py | Python | mit | 71,168 | [
"VisIt"
] | f656a5c6f29c7de5395367b7ed60798a05bcf37542455c4e19026e5b32b76e59 |
#
# Copyright (C) 2001-2008 greg Landrum
#
""" unit testing code for the Doctests
"""
import doctest
import unittest
from rdkit.ML.Data import SplitData, DataUtils
from rdkit.TestRunner import redirect_stdout
from io import StringIO
def load_tests(loader, tests, ignore):
""" Add the Doctests from the module "... | greglandrum/rdkit | rdkit/ML/Data/UnitTestDoctests.py | Python | bsd-3-clause | 1,607 | [
"RDKit"
] | 48aeed741905a8463d8e5411f854876ae5f47569d24cadf6cc3dca379a798c91 |
"""Define all units and constants
"""
from unties.units_group import UnitsGroup
UnitsGroup._locals = globals()
# I don't want to import math just for this...
pi = 3.14159265358979323846264338327950288419716939937510
UnitsGroup.add_prefixes({
# 'Y': [10**24, 'Yotta'],
# 'Z': [10**21, 'Zetta'],
# 'E': [10*... | spejamchr/unties | unties/units.py | Python | mit | 12,062 | [
"Avogadro"
] | 7bb71c75663111704bd5a4e78944e3935487758a71173309030385cce40056d4 |
# gen_deffile.py
# Drew Levin
# August 30, 2015
#
# Generates a .def file for model definition in CyCells. Takes in a list of
# parameters and a file name. The file creation is a side effect.
# parameters is a dictionary of parameter values with keys as defined in
# hypercube.py
import os
def gen_file(params, file... | drewlevin/chemokine | sensitivity/testing/gen_deffile.py | Python | gpl-3.0 | 8,368 | [
"Gaussian"
] | 05d851f8dde2c7361f8e5295f6cb6098af4f00f062890507070aacbd75a4a393 |
# Lint as: python2, python3
# Copyright 2018 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
#
... | mlperf/training_results_v0.7 | Google/benchmarks/transformer/implementations/transformer-research-TF-tpu-v4-16/lingvo/tasks/mt/params/mlperf.py | Python | apache-2.0 | 27,995 | [
"Gaussian"
] | ec2211bb206f8c53029b92b10a23144b5fb20251f4b5d917a44207ef29ee3c28 |
#simulated neuron scalar data provider
import os
import sys
import numpy as np
import scipy.misc
import glob
sys.path.append("../convnet-folk_master")
from w_util import readLines
# define default parameters
DATA_NUM=1000
class SimSet:
def __init__(self, paramfile):
print "SimNeuPrvd: parsing", ... | whereaswhile/DLSR | common/SimNeuPrvd.py | Python | gpl-2.0 | 1,824 | [
"NEURON"
] | fa69f74f6fc87a1ffaba00d422e10546e7fd9748998d34150e1559a5882295ea |
import sap.if1
import sap.symbol_table
import sap.error
class CompilerBase(object):
placeholder = object()
def __init__(self):
self.m = sap.if1.Module()
self.symtab = sap.symbol_table.SymbolTable()
self.error = sap.error.CompilerError(self)
self.graphs = []
for sap_typ... | patmiller/SAP | sap/compiler_base.py | Python | bsd-3-clause | 930 | [
"VisIt"
] | f2e449f5f0c46380bfbfb22eb69e166d8e0b48c11fcf10961d63f1e2e64c456b |
"""
Helper Classes and Functions for docking fingerprint computation.
"""
from __future__ import division
from __future__ import unicode_literals
__author__ = "Bharath Ramsundar and Jacob Durrant"
__license__ = "GNU General Public License"
import logging
import math
import os
import subprocess
import numpy as np
impo... | Agent007/deepchem | deepchem/feat/nnscore_utils.py | Python | mit | 17,258 | [
"RDKit"
] | 2884a4e660b63444c1d422a59309d4f4bb764d67dc5948f34e9a1ce2cae39a3d |
"""Tests for TURBOMOLE cauclator interface."""
import os
import numpy as np
from phonopy.interface.phonopy_yaml import read_cell_yaml
from phonopy.interface.turbomole import read_turbomole
data_dir = os.path.dirname(os.path.abspath(__file__))
def test_read_turbomole():
"""Test read_turbomole."""
cell = rea... | atztogo/phonopy | test/interface/test_TURBOMOLE.py | Python | bsd-3-clause | 760 | [
"TURBOMOLE",
"phonopy"
] | 7aa7f1c7e84f7e6d2b0dc74f8e9cde06ede1fb25b47f7445d833ae925874809a |
# SYSTEM LIBS
from matplotlib.colors import LogNorm
import matplotlib.pyplot as plt; plt.ion();
import matplotlib
import numpy as np
import pandas as pd
# from root_pandas import read_root
import sys
from itertools import islice
from scipy import signal # To find peaks, for edge-detecting the crystal
from scipy.optimiz... | f-forcher/crystal-channeling-analysis | channeling_efficiency.py | Python | gpl-3.0 | 16,737 | [
"CRYSTAL",
"Gaussian"
] | f1dff7234aa1da8e34025c4bcaac5cd4d345998fb71a7982e44e82fef487168a |
class SOM:
"""
A Self-Organnising Map aka Kohonen map.
This class is a wrapper around SOM_PAK.
"""
def __init__(self, data, shape=(12,8), topology='rect', neighbourhood='gaussian'):
"""
Initialises a SOM using the input data set (a list of lists,
or a Numpy array).
... | christiankaiser/sompak-py | sompak/__init__.py | Python | mit | 6,023 | [
"Gaussian"
] | ea65c17823b101e2e56e595dd5282847584e1dda6fda0b6519a338e347dc247b |
# Copyright (c) Geoffrey Lentner 2015. All Rights Reserved.
# See LICENSE (GPLv3)
# slipy/SLiPy/Profile.py
"""
Profile fitting tasks for spectra.
"""
import numpy as np
from scipy.optimize import curve_fit
from scipy.interpolate.interpolate import interp1d
from scipy.special import wofz as w
from scipy.integrate impor... | gLENTNER/SLiPy | SLiPy/Profile.py | Python | gpl-2.0 | 45,178 | [
"Gaussian"
] | 416ae8525fed907526f4e7f498547ee5d9518fae3a27016165a4dc01da881a93 |
########################################################################
# $HeadURL$
# File : BuildCloudinitScript.py
# Author : Victor Mendez
########################################################################
"""
This class construct a cloudinit script for a DIRAC image and IaaS endpoint
"""
import os
im... | myco/VMDIRAC | WorkloadManagementSystem/Client/BuildCloudinitScript.py | Python | gpl-3.0 | 7,487 | [
"DIRAC"
] | ec16ae6c9b940f6b953bfaafcde1d99ab6e040b46852be0757ae7f4855bf6b74 |
#!/usr/bin/python
import numpy as np
import Scientific.IO.NetCDF as nc
import pylab as pl
dFile = nc.NetCDFFile("vScatter.nc", "r")
for hName in dFile.variables.keys():
print dFile.variables[hName].getValue()
# rho = dFile.variables[mName].porosity
# h = dFile.variables[mName].porosityHeight
# print np.me... | dronir/EM | python/plotHemisphere.py | Python | gpl-3.0 | 387 | [
"NetCDF"
] | c03caf7182da1398a1755f8eba1f636a2a401aad14946016970e992377d5237b |
# -*- coding: utf-8 -*-
'''
IMProToo
Improved MRR Processing Tool
Python toolkit to read write and process MRR Data. Raw Data, Average and
Instantaneous Data are supported.
This file includes some helper functions
Copyright (C) 2011-2021 Maximilian Maahn, U Leipzig
maximilian.maahn_AT_uni-leipzig.de
https://github.c... | maahn/IMProToo | IMProToo/tools.py | Python | gpl-3.0 | 7,861 | [
"NetCDF"
] | 724fd0ece4697c608bffeadbd9b6242066ec3f2d2b211d10a26ddfc5e52ce832 |
'''
fs.contrib.tahoefs
==================
Example (it will use publicly available, but slow-as-hell Tahoe-LAFS cloud):
from fs.contrib.tahoefs import TahoeFS, Connection
dircap = TahoeFS.createdircap(webapi='http://pubgrid.tahoe-lafs.org')
print "Your dircap (unique key to your storage directory... | atty303/pyfilesystem | fs/contrib/tahoefs/__init__.py | Python | bsd-3-clause | 16,384 | [
"VisIt"
] | 577a835400c1c778a678077e8c3494bccce343a2a5b0301c1afa94ace6ce4eb1 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# transistorAmp.py
#
# Copyright 2015 Roberto Tavares <roberto.tavares.filho@gmail.com>
#
# Versão: 0.1, em 07/09/2015
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published b... | cadele/cadele | transistorAmp.py | Python | gpl-2.0 | 21,912 | [
"VisIt"
] | c4b49318fb919d5254d88fdec1527dc4cccc5534f897faa8b4a72ea0ca1c98a3 |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _
from zeroinstall.support import tasks
from zeroinstall.injector import handler, download
gobject = tasks.get_loop().gobject
glib = tasks.get_loop().glib
version = '2.4-rc1-post'
class GUIH... | linuxmidhun/0install | zeroinstall/gui/gui.py | Python | lgpl-2.1 | 3,008 | [
"VisIt"
] | 8b40e8afa58a412c27ae73950e235813d894b0b16bd9853c9a323ac3c9bc7b70 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/bouqueteditor/web/getservices.py | Python | gpl-2.0 | 6,302 | [
"VisIt"
] | 9cb7930848b566c7652ae4c6fd5ae6388b857b16f4b37e208d9cc6de6e83f344 |
# -*- coding: utf-8 -*-
# creates: diffusion-I.png diffusion-T.png diffusion-F.png diffusion-barrier.png
#import matplotlib
#matplotlib.use('Agg')
import pylab as plt
from ase.io import read, write
from ase.neb import fit
if 1:
execfile('diffusion1.py')
execfile('diffusion2.py')
execfile('diffusion4.py')... | askhl/ase | doc/tutorials/neb/diffusion.py | Python | gpl-2.0 | 973 | [
"ASE"
] | 9b59d1491af9413feb96828a9652e71b66007523dc5eb27e6dc087a94b7a1567 |
#
# Copyright (C) 2001,2002,2003 greg Landrum and Rational Discovery LLC
#
""" Functionality for ranking bits using info gains
**Definitions used in this module**
- *sequence*: an object capable of containing other objects which supports
__getitem__() and __len__(). Examples of these include lists, tupl... | rdkit/rdkit-orig | rdkit/ML/InfoTheory/BitRank.py | Python | bsd-3-clause | 5,509 | [
"RDKit"
] | 1c649bb28ee68f8b9ab75333f20501601b30fa5267ca502f0a1c645468ad024c |
# Orca
#
# Copyright 2004-2009 Sun Microsystems Inc.
# Copyright 2010-2013 The Orca Team
#
# 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... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/messages.py | Python | gpl-3.0 | 95,927 | [
"ORCA"
] | 1d0a4a4a7d377ea46f52b4a6829d3da1238e2f567046db4c28ec57212086de83 |
'''
Plots the normalized absolute value of the bias of triple collocation after CDF matching in the linear Gaussian case
The error model and notation are explained in evaluateCDFBiasLinearGaussian
The bias is normalized by scaling it:
- with respect to the standard deviation of the noise (normalization = 'noise')
... | szwieback/nlscaling | CDFAnalyticalBias/plotCDFBiasLinearGaussian.py | Python | gpl-3.0 | 3,466 | [
"Gaussian"
] | 8d64a6cf1d11be23b29c31ba3278858eadade3895178b3dc38bd0d6d4db13d5d |
#!/usr/bin/env python
'''
Description
If using files, (call by command line or from python):
all the inputs are raw float32 vectors files that are reshaped by the number
of f0 values in ff0.
There are three safe patches that were not described in the publication[1]:
(These are not critical, they might re... | gillesdegottex/pulsemodel | synthesis.py | Python | apache-2.0 | 18,626 | [
"DIRAC",
"Gaussian"
] | 90c9ee23b7642d22671d03d16efdbdffcf91e982ca8d5f14f3bd878910a945a9 |
from __future__ import print_function
import sys
import random
import os
from builtins import range
import time
import json
sys.path.insert(1, "../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.naive_bayes import H2ONaiveBayesEstimator
from h2o.grid.grid_search import H2OGridSearch
class Tes... | h2oai/h2o-3 | h2o-py/dynamic_tests/testdir_algos/naivebayes/pyunit_naivebayes_gridsearch_over_all_params_large.py | Python | apache-2.0 | 22,200 | [
"Gaussian"
] | 2c619655f82813059da389c095ea686022899a53d5742b51e930bc83222b7604 |
"""
Tests for serial.py.
"""
import cPickle
from cStringIO import StringIO
import gzip
import shutil
import tempfile
import unittest
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit_utils import conformers, serial
class TestMolIO(unittest.TestCase):
"""
Base test class for molecule I/O.
... | skearnes/rdkit-utils | rdkit_utils/tests/test_serial.py | Python | bsd-3-clause | 25,578 | [
"RDKit"
] | d9599d0027567c2f64b6d4e89b2a98de1b444680bf0084f5caf546c706b4083f |
# Orca
#
# Copyright 2014 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# 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 o... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/apps/gedit/spellcheck.py | Python | gpl-3.0 | 2,365 | [
"ORCA"
] | 6ab1317994e98eca91531342f0b13ca01f960847af9f88f9ecbb981847314f2c |
from __future__ import division
from __future__ import print_function
from past.utils import old_div
import sys
sys.path.insert(1, "../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.gam import H2OGeneralizedAdditiveEstimator
# In this test, we check and make sure that we can do scoring
def test... | h2oai/h2o-3 | h2o-py/tests/testdir_algos/gam/pyunit_PUBDEV_7708_check_lambda_min_ratios.py | Python | apache-2.0 | 1,958 | [
"Gaussian"
] | c02d8a0c6bf9dafebad2070dc60375df3f1f823d95a0748f84920d4876673cf2 |
"""Generating random numbers."""
import numpy as np
def test_run():
# Generate an array full of random numbers, uniformly distributed from [0.0, 1.0)
print np.random.random((5, 4))
# Sample from a Gaussian distribution
print np.random.normal(size = (2, 3))# standard normal (mean = 0, ... | bluemurder/mlfl | udacity course code/01-03-numpyrandomarrays.py | Python | mit | 737 | [
"Gaussian"
] | 775ed1eb74614c1dc7023a76720425bef6c1f5acba53e17614d240a0d89f819d |
# Copyright (c) 2019 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
from absl import app
from selenium.webdriver.common.by import By
from selenium.webdriver.support import expected_conditions
from selenium.webdriver.suppo... | ric2b/Vivaldi-browser | chromium/chrome/test/enterprise/e2e/policy/allow_deleting_browser_history/allow_deleting_browser_history_webdriver_test.py | Python | bsd-3-clause | 1,991 | [
"VisIt"
] | 08f1465a129b57a9b6434aded573276e061fc0c61c4194e70090debfda95cba3 |
# test on word2vec package
import os
import sys
reload(sys)
import random
import multiprocessing
import gensim, logging
logging.basicConfig(format='%(asctime)s : %(levelname)s : %(message)s', level=logging.INFO)
import numpy as np
from gensim.models import Word2Vec
from gensim.models.word2vec import LineSentence
c... | sufengniu/kaggle_ai2 | word_embedding.py | Python | mit | 1,611 | [
"NEURON"
] | 04bb4c2745793acb05199e906b185ea468a6d5ee819ab2facfd37a6fe7621a5b |
import os
from os.path import splitext, basename, abspath, dirname, join
import h5py
import logging
# noinspection PyUnresolvedReferences
from rdkit import Chem
from datatypes.objects import Properties, Molecule
from datatypes.strings import Smiles
def set_createdb_parser(root):
createdb = root.add_parser ( "creat... | sergsb/clever | processing/hdf5creator.py | Python | apache-2.0 | 1,931 | [
"RDKit"
] | 0edead7d5f9a09f7a2950402be26924dcf3e714e9edc8bb50443568ef085c70b |
# -*- coding: utf-8 -*-
# ------------------------------------------------------------
# streamondemand.- XBMC Plugin
# Canal para asiansubita
# http://www.mimediacenter.info/foro/viewforum.php?f=36
# ------------------------------------------------------------
import re
import urlparse
from core import logger
from co... | costadorione/purestream | channels/asiansubita.py | Python | gpl-3.0 | 5,847 | [
"ADF"
] | 04732b23197e2ceb09be0a131c0d0c4c9ffc4846bab27315b5f322856c304caa |
#!/usr/bin/python
"""
" @section DESCRIPTION
" RF model classes
"""
import os
import copy
import numpy as np
from operator import mul
from time import time, sleep
from scipy.ndimage import correlate as im_corr
import plotting.plotting_functions as plt_fun
import rf_obj_funs_and_grads as rf_obj_fun
import rf_optimizat... | JohanWesto/receptive-field-models | rf_models/rf_models.py | Python | mit | 58,351 | [
"Gaussian"
] | 708dd801e4bcb182e0b98b73a3deb22d459ee55231dc115312579c2384a264c5 |
from flyingpigeon import visualisation as vs
from pywps.Process import WPSProcess
class VisualisationProcess(WPSProcess):
def __init__(self):
# definition of this process
WPSProcess.__init__(self,
identifier = "visualisation",
title="Visualisation of netcdf files",
... | sradanov/flyingpigeon | flyingpigeon/processes/wps_visualisation.py | Python | apache-2.0 | 2,787 | [
"NetCDF"
] | e13b1ecae60c6898c3ca8a5158be743da26eec4a53535f3bcf82da087251b50b |
#
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2007, 2015, Oracle and/or its affiliates. All rights reserved.
# DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS FILE HEADER.
#
# This code is free software; you can redistribute it and/or modify ... | md-5/jdk10 | src/jdk.internal.vm.compiler/.mx.graal/mx_graal.py | Python | gpl-2.0 | 1,547 | [
"VisIt"
] | 863ca0fd4856c040ac353e9786dccba4114c2e2b722c3cc756e4353cb0056217 |
#!/usr/bin/python
#
# Copyright (C) 2010 The ESPResSo project
# Copyright (C) 2008 Axel Arnold
#
# 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 o... | roehm/cython | tools/trace_memory.py | Python | gpl-3.0 | 2,219 | [
"ESPResSo"
] | c7e255d1ed3b25e9e8231e242dae4465b245e19d1bffc71c70fc315715229b49 |
import numpy as np
_merra2_long_res = 0.625
_merra2_lat_res = 0.5
def get_surrounding_merra2_nodes(long, lat, grid=False):
"""
Calculates four surrounding MERRA2 nodes for the given coordinate.
Returns a string of long for ncks, string of long for ncks
"""
# Round to the appropriate resolution
... | sailorsenergy/windb2 | windb2/model/merra2/util.py | Python | gpl-3.0 | 12,108 | [
"NetCDF"
] | db5b8b943f122a76f8ffa682f0c862a95aba196b0479a61604742b12a3ea8fea |
# coding: utf-8
"""
===================================
Enhanced chroma and chroma variants
===================================
This notebook demonstrates a variety of techniques for enhancing chroma features and
also, introduces chroma variants implemented in librosa.
"""
##########################################... | librosa/librosa | docs/examples/plot_chroma.py | Python | isc | 7,136 | [
"Brian"
] | e791217d16a60c4c3edcea95dc43d136f2ab135d3e551214dcc58425328621f3 |
from __future__ import print_function, division
import matplotlib
matplotlib.use('agg')
from nutils import *
import scipy
import numpy as np
import matplotlib.pyplot as plt
from scipy import sparse
from scipy.io import mmwrite
from mskrylov import poly_driver, nested_driver
from mekrylov import me_driver
import time
... | ManuelMBaumann/freqdom_compare | python_code/elast_squares.py | Python | mit | 11,705 | [
"VTK"
] | 60d795799f93dd81cfbffb8cf2eba711e32d43a297a29805aa98c03a37c7473f |
"""
Copyright (c) 2015 Red Hat, Inc
All rights reserved.
This software may be modified and distributed under the terms
of the BSD license. See the LICENSE file for details.
"""
from __future__ import print_function, absolute_import, unicode_literals
import json
import os
import logging
from requests.utils import gues... | bfontecc007/osbs-client | osbs/cli/capture.py | Python | bsd-3-clause | 3,426 | [
"VisIt"
] | 4f323443e919183206cd904e667bd38c639e5bf96fda3056413fa7135c51a615 |
def alignImage(static, moving, level_iters):
"""The Symmetric Normalization algorithm uses a multi-resolution approach by building a Gaussian Pyramid.
The static image is used a reference; a transformation that transforms the moving image into the
static image is found and applied to the static image. Retu... | wesleybeckner/afm-miner | afmMiner/alignimages.py | Python | mit | 1,747 | [
"Gaussian"
] | 4537509e10cb79030b3bcad71e49d67f761d912fd69f769bccd0dbf82921fc8c |
import platform, os, re
import subprocess
from mooseutils import colorText
from collections import namedtuple
import json
from tempfile import TemporaryFile
TERM_COLS = 110
LIBMESH_OPTIONS = {
'mesh_mode' : { 're_option' : r'#define\s+LIBMESH_ENABLE_PARMESH\s+(\d+)',
'default' : 'REPLICATE... | liuwenf/moose | python/TestHarness/util.py | Python | lgpl-2.1 | 25,575 | [
"VTK"
] | 64de2b9f40ab74d230bcd464d4d3f4d1e09f4689a19421fb545593434dcc5cb6 |
# -*- coding: utf-8 -*-
# FOGLAMP_BEGIN
# See: http://foglamp.readthedocs.io/
# FOGLAMP_END
import asyncio
import time
import json
import logging
import socket
import subprocess
from aiohttp import web
from foglamp.common import logger
from foglamp.services.core import server
from foglamp.services.core.api.statisti... | foglamp/FogLAMP | python/foglamp/services/core/api/common.py | Python | apache-2.0 | 6,018 | [
"Amber"
] | 256da2bf55666afc135ed86235a3dedb9daced98c696abdb0124e5d0a30e25b8 |
#!/usr/bin/env python
import Command
import recalboxFiles
import zipfile
import shutil
from generators.Generator import Generator
import fsuaeControllers
from os import path
class FsuaeGenerator(Generator):
# from one file (x1.zip), get the list of all existing files with the same extension + last char (as number... | nadenislamarre/recalbox-configgen | configgen/generators/fsuae/fsuaeGenerator.py | Python | mit | 4,372 | [
"ADF"
] | 36a81e0386193751052bb2ca787620a14d68d3c70a43f1216f65d4cc1819d18f |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/songs/lib/openlyricsexport.py | Python | gpl-2.0 | 4,459 | [
"Brian"
] | 24c6584b4e693ea37ce7c5bbe26c753340753bddba935997c0f68cc34029e09c |
# -*- coding: utf-8 -*-
#
# test_siegert_neuron.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 of the Lic... | hesam-setareh/nest-simulator | pynest/nest/tests/test_siegert_neuron.py | Python | gpl-2.0 | 4,811 | [
"NEURON"
] | 69e5c78c2ce4a82c3de2b2c8321ed6cf69652b42b53ec55eb3536662a97530fb |
# Copyright (C) 2013 Matthew C. Zwier, Joshua L. Adelman and Lillian T. Chong (see note below).
#
# This file is part of WESTPA.
#
# WESTPA 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 t... | ajoshpratt/westpa | lib/wwmgr/work_managers/core.py | Python | gpl-3.0 | 16,963 | [
"Brian"
] | 00de6cc1b47828d5354c75477fb516d9f6e596e2d833c4c99e706119324ed9e5 |
"""
State Space Model
Author: Chad Fulton
License: Simplified-BSD
"""
from __future__ import division, absolute_import, print_function
import numpy as np
import pandas as pd
from scipy.stats import norm
from .kalman_smoother import KalmanSmoother, SmootherResults
from .kalman_filter import (
KalmanFilter, Filter... | kiyoto/statsmodels | statsmodels/tsa/statespace/mlemodel.py | Python | bsd-3-clause | 88,741 | [
"Gaussian"
] | b2f969aa6d137b362b0617dee1501f51baff8f1576c003516eda974fe8ba2f42 |
"""
The GA4GH data model. Defines all the methods required to translate
data in existing formats into GA4GH protocol types.
"""
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
import base64
import collections
import glob
import json
import os
import ga4gh.... | saupchurch/server | ga4gh/server/datamodel/__init__.py | Python | apache-2.0 | 22,507 | [
"pysam"
] | 22634f66058b9b49d2d38c84ab8e9ad9699957d8b85af06bcc444c227d43029d |
# Orca
#
# Copyright (C) 2010 Joanmarie Diggs
# Copyright (C) 2011-2012 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# 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; eith... | GNOME/orca | src/orca/scripts/toolkits/WebKitGtk/script_utilities.py | Python | lgpl-2.1 | 9,888 | [
"ORCA"
] | 2a116e1bfbd324765ec3c7c946aa02db92beb1395947f05859d62876f7ded99c |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2010, 2011, 2012, 2013, 2014 CERN.
#
# Invenio is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 2 of the
# License, or (a... | zenodo/invenio | invenio/legacy/batchuploader/engine.py | Python | gpl-2.0 | 29,447 | [
"VisIt"
] | b5e5c843326ccee4e7d7f2f6f2335d43102081cc27b82b18614f3cdd0414f1ed |
#!/usr/bin/env python
"""[License: GNU General Public License v3 (GPLv3)]
This file is part of FuMa.
FuMa 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 opti... | yhoogstrate/fuma | setup.py | Python | gpl-3.0 | 2,283 | [
"HTSeq"
] | e8fa9a58a2a5d7899047a1dae239fff6a12f56db32b5fe723ef344a604a7f79e |
#! /usr/bin/env python
#
# Copyright (C) 2015-2016 Rich Lewis <rl403@cam.ac.uk>
# License: 3-clause BSD
"""
# skchem.io.sdf
Defining input and output operations for sdf files.
"""
from functools import wraps
import warnings
from rdkit import Chem
import pandas as pd
from ..core import Mol
from ..utils import Suppr... | richlewis42/scikit-chem | skchem/io/sdf.py | Python | bsd-3-clause | 6,101 | [
"RDKit"
] | e4a650d962fa887da97087cd8533d6f9cfdf0fcaebd76aa82f04158b1a75a79f |
# Copyright 2015-2016 Google 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://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law... | wklken/yapf | yapf/yapflib/split_penalty.py | Python | apache-2.0 | 15,677 | [
"VisIt"
] | 7e2e3c979d1e76cfce4e5337a573ceaad8edfc4b8daa5a48e9732ec6b9036bc9 |
# Copyright 2016 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... | tensorflow/tensorflow | tensorflow/python/autograph/core/converter.py | Python | apache-2.0 | 10,788 | [
"VisIt"
] | 46d570684fe6b79297229aec1e5c726d385816877a147619042a33f41f38a7d7 |
import os, sys
import numpy as np
import pysam
DATAPATH="/cs/taatto/group/mlb/synergy/data/2012-03_RNA"
TRANSCRIPTS = ["ENST00000561552", "ENST00000361711", "ENST00000343939", "ENST00000393306", "ENST00000565123", "ENST00000563543", "ENST00000567707", "ENSG00000140961_unspliced"]
UNSPLICED = ["ENSG00000140961_unspli... | ahonkela/pol2rna | python/count_osgin1_reads.py | Python | bsd-3-clause | 2,013 | [
"pysam"
] | d03c4bf27bd6bb12c395df75dc55b92cda4b07820fdd00514f4d962664ebe7cb |
'''
VAE that associate latent representations for different modals of sensory data
'''
import os
import time
import datetime
import numpy as np
from itertools import combinations
import tensorflow as tf
def xavier_init(fan_in, fan_out, constant=1):
""" Xavier initialization of network weights"""
# https://stac... | navigator8972/vae_hwmotion | vae_assoc.py | Python | gpl-3.0 | 30,163 | [
"Gaussian"
] | 206a9644ce7caba6295051ee2851527a5db22226e071d4b09b6de64aabfffeaf |
# Authors : Denis A. Engemann <denis.engemann@gmail.com>
# Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
#
# License : BSD 3-clause
from copy import deepcopy
import math
import numpy as np
from scipy import fftpack
# XXX explore cuda optimization at some point.
from ..io.pick import _pick_dat... | adykstra/mne-python | mne/time_frequency/_stockwell.py | Python | bsd-3-clause | 10,013 | [
"Gaussian"
] | b94fa9ddae26a7dad822985b02a7f499db5abe117de7451f5a17a9ac81bc052f |
# -*- coding: utf-8 -*-
"""
Created on Tue Jan 30 21:01:59 2018
@author: mhangaard
"""
import numpy as np
from ase.build import bulk
from catkit.surface import SlabGenerator
from ase.build import add_adsorbate
from ase.data import covalent_radii
from atoml.fingerprint.adsorbate_prep import get_radius, autogen_info
fro... | jboes/CatKit | docs/tutorials/9_adsorbate_fingerprints.py | Python | gpl-3.0 | 3,329 | [
"ASE"
] | 61d8e50986964575c5c6c930acb244c190baa4df9f1358077d56fd9d52cef1ef |
import os
import shutil
import sys
import glob
from setuptools import setup, find_packages
def read(fname):
return open(os.path.join(os.path.dirname(__file__), fname)).read()
version = 'x.y.z'
if os.path.exists('VERSION'):
version = open('VERSION').read().strip()
setup(
name='saffrontree',
version=vers... | andrewjpage/saffrontree | setup.py | Python | gpl-3.0 | 1,270 | [
"Biopython"
] | e72c9a8bf04646f48d76af4e57de803b0cd8b6488a3bec223dd523494689bd59 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import warnings
import numpy as np
from pymatgen.core.composition import Composition
from pymatgen.core.periodic_table import DummySpecies, Element, Species
from pymatgen.core.lattice import ... | gmatteo/pymatgen | pymatgen/io/tests/test_cif.py | Python | mit | 44,924 | [
"ABINIT",
"VASP",
"pymatgen"
] | 90cbf9f9c818c409e47a57e36e641b43b5b64fd431a38a69728e2732317d8918 |
# -*- coding: utf-8 -*-
"""
====================
1D optimal transport
====================
This example illustrates the computation of EMD and Sinkhorn transport plans
and their visualization.
"""
# Author: Remi Flamary <remi.flamary@unice.fr>
#
# License: MIT License
import numpy as np
import matplotlib.pylab as p... | rflamary/POT | examples/plot_OT_1D.py | Python | mit | 1,698 | [
"Gaussian"
] | f59f6ecafb992db0c9a1ab80eae1643cd3e7d4205cb9b8bc3581ea42739e2cca |
from __future__ import print_function
import numpy as np
import mdtraj as md
from mdtraj.testing import get_fn, eq, skipif
from mdtraj.nmr.shift_wrappers import find_executable, SPARTA_PLUS, PPM, SHIFTX2
from mdtraj.utils import six
@skipif(not find_executable(SPARTA_PLUS), 'SPARTA+ binary not found')
def test_spartap... | daviddesancho/mdtraj | mdtraj/tests/test_nmr.py | Python | lgpl-2.1 | 3,237 | [
"MDTraj"
] | 504b5148ea8fa9d033a9aad93591fffd111534f369cd5e12cb9652ff291549c5 |
from django.conf import settings
from copy import copy
from django.core.exceptions import ImproperlyConfigured
class AdminExcludeFieldsMixin(object):
visit_model = None
visit_attr = None
visit_codes = {}
def __init__(self, *args, **kwargs):
super(AdminExcludeFieldsMixin, self).__init__(*args... | botswana-harvard/edc-admin-exclude | edc_admin_exclude/admin.py | Python | gpl-2.0 | 5,423 | [
"VisIt"
] | 784388e45e6ad43cae1a9ed103ec20b4da58c697c9dff5162b21eb7dc848a0b2 |
# -*- coding: utf-8 -*-
""" Incident Reporting System - Model
@author: Sahana Taiwan Team
"""
module = "irs"
if deployment_settings.has_module(module):
# ---------------------------------------------------------------------
# List of Incident Categories
# NB It is important that the meaning of thes... | ksetyadi/Sahana-Eden | models/06_irs.py | Python | mit | 28,097 | [
"VisIt"
] | 29a3a9e3481481db5876718f3cfe5f324a89142ec2260b0479288c94b7dba669 |
#!/usr/bin/python
import os, sys
import argparse
# Locate the moose/python directory
sys.path.append(os.path.join(os.path.abspath('..'), 'python'))
# Load the required moose/python packages
from FactorySystem import ParseGetPot
from PresentationBuilder import base
if __name__ == '__main__':
# Create the argument ... | danielru/moose | scripts/presentation_builder.py | Python | lgpl-2.1 | 746 | [
"MOOSE"
] | d49b7888c1afded8a733b68499e89f38676ad722c6c74cf5fe854b0874774775 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import os
import subprocess
import sys
# Version check prior to non-stdlib imports
if sys.version_info < (3, 5):
sys.stderr.write(
"ERROR: mapDamage requires Python v3.5 or above, but "
"Python v%i.%i was used\n" % sys.version_info[:2]
)
sys.ex... | ginolhac/mapDamage | setup.py | Python | mit | 1,986 | [
"pysam"
] | de2ffa0d386b85193fddd8ca7806b8f4d765302cf0d36aeea998889259242b68 |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/storage/__init__.py | Python | gpl-3.0 | 1,149 | [
"ESPResSo"
] | 9a4f53036baf0191927e9d22cee4aa3327ab91a7d09eb4ff2713ecf95d9418bb |
# -*- coding: utf-8 -*-
import logging
import sys
import numpy as np
from itertools import tee, izip
import llvm.core as lc
import llvm.passes as lp
import llvm.ee as le
from core_translator import CoreTranslator
from type_inference import TypeInfer, UnderDeteremined
from type_system import TVar, TFun, int32, int64,... | tartavull/fastpy | fastpy/fastpy.py | Python | mit | 4,343 | [
"VisIt"
] | a618fe99c2891e2c7eb2075cd4223ddf186fdcb65640c465b6ac436ad825994f |
# coding=utf-8
# Copyright 2016 Google 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://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by app... | corona10/grumpy | grumpy-tools-src/grumpy_tools/compiler/imputil_test.py | Python | apache-2.0 | 13,859 | [
"VisIt"
] | 9ab8b390aa5b91a9e86670527d70ab4f860dd97c7f38e559821726f164027bc8 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright 2010 British Broadcasting Corporation and Kamaelia Contributors(1)
#
# (1) Kamaelia Contributors are listed in the AUTHORS file and at
# http://www.kamaelia.org/AUTHORS - please extend this file,
# not this notice.
#
# Licensed under the Apache License,... | sparkslabs/kamaelia | Sketches/MPS/BugReports/FixTests/Kamaelia/Kamaelia/Device/DVB/Parse/ParseNetworkInformationTable.py | Python | apache-2.0 | 25,045 | [
"CRYSTAL"
] | edbd4519a0f86693300ed533f81c5d99b2514a26b1478fa55f740a66297d88ee |
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