text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
from TestHa... | nuclear-wizard/moose | python/TestHarness/tests/test_DistributedMesh.py | Python | lgpl-2.1 | 1,112 | [
"MOOSE"
] | 8a5e06319a25f85e2fa45a3aee2cb6b158b320af2e9b480bcce96b28a249deea |
import sys
import base64
import os
import pytest
import shutil
import subprocess
import yaml
yaml_loader = yaml.SafeLoader
yaml_dumper = yaml.SafeDumper
try:
yaml_loader = yaml.CSafeLoader
yaml_dumper = yaml.CSafeDumper
except AttributeError:
pass
from typing import Any, ClassVar, Dict, List, Optional, ... | datawire/ambassador | python/tests/kat/abstract_tests.py | Python | apache-2.0 | 16,480 | [
"VisIt"
] | 12bd9db03fc32c25460542cc1975f013b109257478d7d8efccee067b53239329 |
#!/usr/bin/python
#Audio Tools, a module and set of tools for manipulating audio data
#Copyright (C) 2007-2012 Brian Langenberger
#This program is free software; you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation; either version 2... | R-a-dio/python-audio-tools | audiotools/m4a_atoms.py | Python | gpl-2.0 | 68,744 | [
"Brian"
] | bd34d2a966c38d8ec9ca0bc7c80982dfdc7b1775bacdedc0f9bebb3b23a12e06 |
"""
Courseware views functions
"""
import logging
import urllib
import json
from datetime import datetime
from django.utils.translation import ugettext as _
from django.conf import settings
from django.core.context_processors import csrf
from django.core.exceptions import PermissionDenied
from django.core.urlresolve... | xingyepei/edx-platform | lms/djangoapps/courseware/views.py | Python | agpl-3.0 | 59,567 | [
"VisIt"
] | b7b5aefaaefb0e60e4e48274f7c09b18b1c7b44cc1925912254ed0f2947a47bf |
# Copyright 2014 Roberto Brian Sarrionandia
#
# 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 t... | sarrionandia/tournatrack | trackpanel.py | Python | apache-2.0 | 2,563 | [
"Brian"
] | 30856d498cd64c6da551666bfeadb41baafa3cb7db9e2fc770c148e0b658ad1e |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Module for graph representations of crystals.
"""
import warnings
import subprocess
import numpy as np
import os.path
import copy
from itertools import combinations
from pymatgen.core import Structure, La... | gVallverdu/pymatgen | pymatgen/analysis/graphs.py | Python | mit | 113,489 | [
"CRYSTAL",
"Jmol",
"pymatgen"
] | 0b2dc80764b22f909d1313320fd0429d6aab6e2c0a8ad21f28ed82171bb5b9fe |
#!/usr/bin/env python
# -----------------------------------------------------------------------------
# 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.
# --------------------... | JWDebelius/scikit-bio | skbio/parse/sequences/tests/test_qseq.py | Python | bsd-3-clause | 6,854 | [
"scikit-bio"
] | 00d1670cc846eb64066145ec33445722d2486a32ff05c31231c4668117120c2a |
#Copyright (c) 2016 Vidhya, Nandini
#Following code is available for use under MIT license. Please see the LICENSE file for details.
#This file implements the scikit version of Gaussian Naive Bayes classification for our data set. It calls the GetData function of the BalanceData module to obtain the training features ... | vidhyal/WitchMusic | GaussianNB.py | Python | mit | 2,107 | [
"Gaussian"
] | 1d217d5b4489f553508e7258c45ce244a82c9861ce51a08ee4527eaa5b6f7a68 |
# Get the best Blast hits from a tab file based on their Bitscore and Identity % (in case of tie keeps all hits).
# e.g. python3 blast_tab_parser.py input.tab output.tab
import sys
def parse_file(input_file):
inputFile = open(input_file, "r")
loci = []
matches = []
bitscores = []
save_lines = dic... | CoBiG2/RAD_Tools | blast_tab_parser.py | Python | gpl-3.0 | 1,798 | [
"BLAST"
] | 6940c571b1b8638c8f45b1a186c5f8c04014878d173cdcafdcc7ca0663cda817 |
def get_dico():
return [
"password",
"123456",
"12345678",
"1234",
"qwerty",
"12345",
"dragon",
"pussy",
"baseball",
"football",
"letmein",
"monkey",
"696969",
"abc123",
"mustang",
"michael",
"shadow",
"master",
"jennifer",
"111111",
"2000",
"jordan",
"superman",
"harley",
"1234567",
"fuckme... | theoneandonly-vector/LaZagne | Windows/src/LaZagne/config/dico.py | Python | lgpl-3.0 | 5,623 | [
"Brian",
"CRYSTAL",
"Jaguar"
] | a820d454798cecababfc6b52b3e819b80adb830905bd01eecbff50087c44e455 |
#
# Copyright (C) 2008, Brian Tanner
#
#http://rl-glue-ext.googlecode.com/
#
# Licensed under the Apache License, Version 2.0 (the "License")
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | GarethNelson/rl-glue-ext | projects/codecs/Python/src/tests/test_rl_episode_experiment.py | Python | apache-2.0 | 1,682 | [
"Brian"
] | b08e550204dd4f3292b222f6cd746d5485d6af2adf5a1b68e5d20546a04c4684 |
# -*- coding: utf-8 -*-
from typing import Any, DefaultDict, Dict, List, Optional, Set, Tuple, Union
from collections import namedtuple, defaultdict
from itertools import chain, islice
from functools import partial
from networkx import Graph, single_source_shortest_path
from django.db import connection
from django.h... | catmaid/CATMAID | django/applications/catmaid/control/analytics.py | Python | gpl-3.0 | 16,171 | [
"NEURON"
] | f138f206777233f187e403b3d35b690a5a84a5eb58829af7eeab4655c49ac8dc |
from __future__ import print_function
import numpy as np
import matplotlib.pyplot as plt
import time
from max_ent_functions import calc_A, calc_K, root_finding_newton, root_finding_diag, max_likelihood_estimate
plt.rc('image',interpolation='nearest',origin='lower')
#set seed for noise for G
seed = 50
# define par... | maxweber1988/Maximum-entropy | code/max_ent.py | Python | gpl-2.0 | 2,121 | [
"Gaussian"
] | de9bdcae0fefcc2c45a40c3c2cd29d85ee92cb71f8021d9eb0a1f14f3972bcfc |
# rio_say
from random import choice
from cowpy import cow
__version__ = '1.1.0'
def moothedata(metadata, key=None):
keys = list(metadata.keys())
# Blacklist metadata items that cows can't pronounce.
blacklist = ['transform', 'affine']
for k in blacklist:
if k in keys:
keys.remo... | perrygeo/rio-plugin-example | metasay/__init__.py | Python | mit | 444 | [
"MOOSE"
] | ceb3b876352e68eac672c9b2c0863480884080ef9deebbe2abc5b7589f2c489e |
from __future__ import division, absolute_import, print_function
import numpy as np
from numpy.testing import (
TestCase, run_module_suite, assert_, assert_raises, assert_equal,
assert_warns, assert_array_equal, assert_array_almost_equal)
from numpy import random
from numpy.compat import asbytes
import... | argriffing/numpy | numpy/random/tests/test_random.py | Python | bsd-3-clause | 60,029 | [
"Gaussian"
] | dfccf7cfb8d7688365b7a83780ef2b89a180df12537ac7714002c99b9f377133 |
import logging
import os
import sys
from tool_shed.util import common_util
import tool_shed.util.shed_util_common as suc
log = logging.getLogger( __name__ )
class EnvManager( object ):
def __init__( self, app ):
self.app = app
def create_env_var_dict( self, elem, install_environment ):
env_... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/env_manager.py | Python | gpl-3.0 | 9,458 | [
"Galaxy"
] | 04cb9890cabad165e7a58e8842a8557bf7c368a8f95d43218611832afc935900 |
#
# Test executable to exercise the Gauss-Hermite class
#
# Copyright (c) 2013 RadiaBeam Technologies. All rights reserved
#
# python imports
import math
# SciPy imports
import numpy as np
import matplotlib.pyplot as plt
# RadiaBeam imports
from radtrack.fields import RbGaussHermiteMN
from radtrack.util import plotTo... | radiasoft/radtrack | experimental/hermite/testHermite01.py | Python | apache-2.0 | 5,179 | [
"Gaussian"
] | e413e2c53571ee5eed469c371aaeab7046e542f73b31cfd109afbcdfe82416ac |
# 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... | kevin-coder/tensorflow-fork | tensorflow/python/autograph/converters/side_effect_guards.py | Python | apache-2.0 | 7,527 | [
"VisIt"
] | 881f105dc554f4f3a4c3719ae5ea5c7368448ca0ca0509b5eb3a86c399693077 |
"""None"""
import time
import os
import numpy as np
from sklearn.grid_search import ParameterGrid
from sklearn.base import clone
from sklearn.gaussian_process import GaussianProcess
from scipy.stats import norm
from joblib import Parallel, delayed
from utils.state import _save
from utils.functions import gaussian... | ivannz/study_notes | year_15_16/thesis/notebooks/gaussian_exp_2d.py | Python | mit | 6,670 | [
"Gaussian"
] | aa723be53184653a0499bd0b3b6cdd9e318d3fb4e57ffdd99060dc2a16be8f18 |
#
# Copyright 2021 Lars Pastewka (U. Freiburg)
# 2020 Thomas Reichenbach (Fraunhofer IWM)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Pub... | libAtoms/matscipy | examples/pressure_coupling/restart_equilibrate_pressure.py | Python | lgpl-2.1 | 3,275 | [
"ASE",
"Matscipy"
] | f91c82ebb7275758dd5db434172892c58747e6abcd6361f8912edab8e934d5f0 |
#!/opt/local/bin/python
"""
Find the outlet location of basins in a grid
"""
from future import print_function
import numpy as np
from netCDF4 import Dataset
import time as tm
from argparse import ArgumentParser, RawTextHelpFormatter
import os
import sys
# -------------------------------------------------------------... | bartnijssen/RVIC | tools/find_pour_points.py | Python | gpl-3.0 | 12,310 | [
"NetCDF"
] | fdf59edad08c8e962d3521cd763aeac765c10ddabf4a32bcd8445e389f416011 |
# -*- coding: utf-8 -*-
"""
Regression tests for the Test Client, especially the customized assertions.
"""
from __future__ import unicode_literals
import datetime
import itertools
import os
from django.contrib.auth.models import User
from django.contrib.auth.signals import user_logged_in, user_logged_out
from django... | ytjiang/django | tests/test_client_regress/tests.py | Python | bsd-3-clause | 67,165 | [
"VisIt"
] | 0482573b503e616fc0caebd425495ab7a6abab0d853143c43dc100a4aef4f97c |
# -*- coding: utf-8 -*-
# Spearmint
#
# Academic and Non-Commercial Research Use Software License and Terms
# of Use
#
# Spearmint is a software package to perform Bayesian optimization
# according to specific algorithms (the “Software”). The Software is
# designed to automatically run experiments (thus the code name
... | DavidMcDonald1993/ghsom | spearmint/spearmint/utils/priors.py | Python | gpl-2.0 | 17,339 | [
"Gaussian"
] | e3a890e65346adeb16903daf8807a98fbf7c461dba52f9a2255dcb356f335ca4 |
# -*- coding: utf-8 -*-
import numpy
import pytest
import pysteps
def _generic_interface_test(method_getter, valid_names_func_pair, invalid_names):
for name, expected_function in valid_names_func_pair:
error_message = "Error getting '{}' function.".format(name)
assert method_getter(name) == expe... | pySTEPS/pysteps | pysteps/tests/test_interfaces.py | Python | bsd-3-clause | 12,151 | [
"Gaussian",
"NetCDF"
] | 7275e725c6ba2970b92e80f951cd84f77ae30cc74cfdf665d99d791a0db68d43 |
#!/usr/bin/env python
#
# Copyright (C) 2014 Brian Caswell <bmc@lungetech.com>
#
# 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 without restriction, including without limitation
# the rights... | f0rki/cb-multios | tools/generate-polls/generator/actions.py | Python | mit | 13,987 | [
"Brian"
] | 1d3d422e2f73501e7f99d48feaf53bf8461a2eca33a6bb8a3ccb90d0bb8e8608 |
from __future__ import division, print_function
import os
import click
import numpy as np
import tqdm
import sklearn.neighbors as skn
import sklearn.gaussian_process as skg
import sklearn.base
import sklearn.metrics
import sklearn.model_selection
import sklearn.preprocessing
import sklearn.pipeline
import sklearn.linea... | Enucatl/machine-learning-aging-brains | local_postprocessing/probability_density_train.py | Python | mit | 6,902 | [
"Gaussian"
] | 818f5a94c8fa7c1b2fea5d230ed38b56c81f225239331a8a00b541862241f9d0 |
############################################################################
#
# Program: GDCM (Grassroots DICOM). A DICOM library
#
# Copyright (c) 2006-2011 Mathieu Malaterre
# All rights reserved.
# See Copyright.txt or http://gdcm.sourceforge.net/Copyright.html for details.
#
# This software is distributed ... | gbook/nidb | src/gdcm/Utilities/VTK/Testing/Python/TestvtkGDCMImageReader2.py | Python | gpl-3.0 | 1,273 | [
"VTK"
] | 692efb7a25ff9e344fdedc94811fb419a641fa8349b9328d8df744807b02ffc5 |
#! /usr/bin/python
# -*- encoding: utf-8 -*-
"""
android UI test framework based on @AndroidViewClient
version 2.0
Copyright (C) 2012-2015 Xinquan Wang
Created on Dec 1, 2012
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtai... | xinquanking/AndJoin | fw/iDevice.py | Python | apache-2.0 | 47,343 | [
"Galaxy"
] | b40cfeb7b8421a34f3d7563e74c2477e1102eb322168ee4fd3647a73fa6dc4a1 |
# Natural Language Toolkit: Expectation Maximization Clusterer
#
# Copyright (C) 2001-2008 University of Pennsylvania
# Author: Trevor Cohn <tacohn@cs.mu.oz.au>
# Porting: Steven Bird <sb@csse.unimelb.edu.au>
# URL: <http://nltk.sf.net>
# For license information, see LICENSE.TXT
from api import *
from util import *
im... | hectormartinez/rougexstem | taln2016/icsisumm-primary-sys34_v1/nltk/nltk-0.9.2/nltk/cluster/em.py | Python | apache-2.0 | 9,506 | [
"Gaussian"
] | 6432bdb8d07b83e47129097778771ba7dc3b65bb20a886ac5da9606d28638d77 |
"""TODO: DOC."""
import os
import platform
from . import bpy
from . import nvb_def
from . import nvb_utils
def NVB_psb_anim_target_poll(self, object):
return nvb_utils.is_mdl_base(object)
def NVB_anim_root_obj_poll(self, object):
return nvb_utils.get_obj_mdl_base(object) is not None
de... | gyoerkaa/mdltools | neverblender/nvb_props.py | Python | gpl-2.0 | 57,071 | [
"BLAST"
] | dc6440171e01bf984a34ab9d69d9fb1746a2c94bbf855b8525c684ef9435d2b4 |
import os
import time
import tempfile
import glob
__doc__ = """ Create/modify a file locally while a file with the same name gets downloaded from the server.
1.7 client has a bug and does not pass this test
2.1.1+ client detects the file being modified locally and restarts itself to complete the sync (which creates... | cernbox/smashbox | lib/test_fileTinkerDownload.py | Python | agpl-3.0 | 3,181 | [
"TINKER"
] | 39309a68293e2e31fe6880f85229933d94f39160d52bde2432db544e5a50fe5d |
from operator import attrgetter
from argparse import ArgumentParser
from netCDF4 import Dataset,date2num
import numpy as np
import datetime
if __name__ == '__main__':
parser = ArgumentParser(description='Extract variables from netcdf file')
parser.add_argument('-i', '--input', required=True, type=str,
... | iaklampanos/bde-pilot-2 | wrf-docker/scripts/ncar_to_ecmwf.py | Python | apache-2.0 | 3,158 | [
"NetCDF"
] | 8ab50fb90ceea7041dcb0809824bc4e1b7d5cdf93a36d627973176580bfc5bde |
# Sample python code to Public API course
# Requires python 3.7+
# Install required dependencies via: $ pip install requests pytz pyrfc3339
from datetime import datetime
from datetime import timedelta
from functools import total_ordering
import os
import platform
import pyrfc3339
import requests
from requests.exceptio... | AquaticInformatics/Examples | TimeSeries/PublicApis/Python/timeseries_client.py | Python | apache-2.0 | 39,309 | [
"VisIt"
] | 1a4534cb8d1e80ae55c29691e16c1428f33b23a9012bc69fecc8a1597b32e6da |
from __future__ import absolute_import, unicode_literals
import json
import requests
import urllib
from datetime import timedelta
from django import forms
from django.conf import settings
from django.contrib.auth import authenticate, login
from django.core.cache import cache
from django.core.paginator import Paginato... | praekelt/rapidpro | temba/api/views.py | Python | agpl-3.0 | 136,478 | [
"VisIt"
] | 130fd6f932649cd61adb7a867693860766b0ae3a873710a8f904e3de8df5274d |
from LMIO.wrapper import *
import matplotlib.pyplot as plt
from easygui import fileopenbox
swcFile = fileopenbox(msg='SWC file with three point soma', filetypes=['*.swc'])
swcFiles = [swcFile]
##*********************************************************************************************************************
## Us... | DaisukeMiyamoto/python-Lmeasure | test/ExampleUsage.py | Python | apache-2.0 | 2,853 | [
"NEURON"
] | aa70b66a044e515132cbc7098e2b5068c2bd2c4b8494a42b1f2954176bdc9f4e |
import sys
class Out:
def write(self, x):
sys.__stdout__.write(x)
raise RuntimeError('not silent')
out, err = sys.stdout, sys.stderr
sys.stdout = sys.stderr = Out()
try:
from gpaw import GPAW, FermiDirac
from ase import Atom, Atoms
a = 5.0
h = 0.2
calc = GPAW(h=h, nbands=1, kp... | ajylee/gpaw-rtxs | gpaw/test/stdout.py | Python | gpl-3.0 | 723 | [
"ASE",
"GPAW"
] | b9dd0ed0146713158cb6a1a718529cba32555e35129e165bb10a540a73da8327 |
import os
project = 'Sagittarius'
########################################
# STARTER KITS
########################################
def build_sk_java():
with ok.root('starter-kits/java'):
ok.maven('compile').maven('package')
def build_sk_javascript():
with ok.root('starter-kits/javascript'):
ok.npm('run build... | willyg302/Sagittarius | okfile.py | Python | mit | 1,988 | [
"GULP"
] | 94edae359bd29bbf9cf02a9b57a37d96d924975bb3693dc133a6c62798902178 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
from unittest import expectedFailure
from common.test.acceptance.tests.helpers import UniqueCourseTest
from common.test.acceptance.pages.lms.auto_auth import AutoAuthPage
from common.test.acceptance.pages.lms.course_info import CourseInfoPage
from common.t... | synergeticsedx/deployment-wipro | common/test/acceptance/tests/lms/test_lms_acid_xblock.py | Python | agpl-3.0 | 5,952 | [
"VisIt"
] | 39b3468333162fb0e874c916720cc1f114343e57e9fed4afde4216768275bf41 |
# Copyright 2015 Adriana Supady
#
# This file is part of fafoom.
#
# Fafoom 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 3 of the License, or
# (at your option) any later... | ptrab/fafoom | fafoom/pyaims.py | Python | gpl-3.0 | 5,631 | [
"FHI-aims"
] | 0d1c140e6887e02072ade9e66d141d99a06d11bc5c5a628d8315578da41ee012 |
#!/usr/bin/env python
'''Class methods representing the neural populations'''
import os
import numpy as np
import LFPy
import neuron
import h5py
import scipy.signal as ss
from scipy.sparse import lil_matrix
from scipy.sparse.linalg import svds
from ViSAPy import CorrelatedNoise, GDF, DriftCell
from matplotlib import cm... | espenhgn/ViSAPy | ViSAPy/cellsimmethods.py | Python | gpl-2.0 | 58,138 | [
"Gaussian",
"NEURON"
] | 96ada6d0641b86ed0d871b876dbcf2541e4c3783cf4d9c47c901306283291ddf |
#!/usr/bin/env python2
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# 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, ei... | niktre/espressopp | examples/adress/hadress_tetraliquid/hadress_tetraliquid_plain/Tetracryst.py | Python | gpl-3.0 | 2,957 | [
"CRYSTAL",
"ESPResSo"
] | 6b46457e6167b532a8c464033a6183163088f4428c98f48b55ec4edd74c66c76 |
#!/usr/bin/env python
"""Processed version of the documentation.
The documentation from the objects of raw_doc is further processed into
objects from the module proc_doc. These objects can then be processed
into structured documents such as HTML more easily.
"""
# TODO(holtgrew): Location traceability for entries an... | h-2/seqan | util/py_lib/seqan/dox/proc_doc.py | Python | bsd-3-clause | 62,903 | [
"VisIt"
] | ee9acbfe089bfeadf90224d03a3c16cff8c520c8c8aa791b61f271fdcb0dc25b |
# -*- coding: utf-8 -*-
from __future__ import print_function, division, absolute_import
try:
import unittest2 as unittest
except ImportError:
import unittest
from datetime import datetime, timedelta
import re
import sys
import socket
import shutil
import os
import json
import tempfile
import contextlib
impo... | Lorquas/subscription-manager | test/test_managercli.py | Python | gpl-2.0 | 95,892 | [
"BLAST"
] | ffba0ab82ae93ac0fc2fd553406d4a30da8663fb945660988f2ffde85c841f17 |
from bs4 import BeautifulSoup
import requests
import re
import random
import tweepy
import shutil
import datetime
import os
import time
from credentials import twitterConsumerKey, twitterConsumerSecret, twitterAccessToken, twitterAccessTokenSecret
global shelterDict
shelterDict = {
'cha': 1004,
'sandco': 319... | mattsteinpreis/CutePetsCbus | fetchParsePost.py | Python | mit | 6,724 | [
"COLUMBUS"
] | 390fa72e94426e31705bb364f87db5faa36f0b56d03fda79863ce4c9a07e5607 |
"""
Implementation of Harwell-Boeing read/write.
At the moment not the full Harwell-Boeing format is supported. Supported
features are:
- assembled, non-symmetric, real matrices
- integer for pointer/indices
- exponential format for float values, and int format
"""
from __future__ import division, print_... | mbayon/TFG-MachineLearning | venv/lib/python3.6/site-packages/scipy/io/harwell_boeing/hb.py | Python | mit | 18,420 | [
"exciting"
] | ff86cb9302df85035258844a8938c1cf26ef4107007e9ab67119fa201f7f4777 |
"""
This is the class that contains the implementation of competitive selective learning
as proposed by Ueda and Nakano in 1993.
"""
import numpy as np
from sklearn.base import BaseEstimator, TransformerMixin
from sklearn.utils import check_array, check_random_state
def _calculate_local_distortion(distortions, cente... | h-mayorquin/time_series_basic | nexa/csl.py | Python | bsd-3-clause | 14,357 | [
"NEURON"
] | cfb8472b01c33d230343e45917e39ecd17ab1c6b471845bb4cc1f8091204bdab |
# cython: infer_types=True
#
# Tree visitor and transform framework
#
import cython
import inspect
import Nodes
import ExprNodes
import Naming
import Errors
import DebugFlags
class TreeVisitor(object):
"""
Base class for writing visitors for a Cython tree, contains utilities for
recursing such trees usi... | bzzzz/cython | Cython/Compiler/Visitor.py | Python | apache-2.0 | 15,306 | [
"VisIt"
] | ff811082338feb1cd3dbbafb12f9ed86f650af51a0949e9104ae54d17c630857 |
# rgToolFactoryMultIn.py
# see https://bitbucket.org/fubar/galaxytoolfactory/wiki/Home
#
# copyright ross lazarus (ross stop lazarus at gmail stop com) May 2012
#
# all rights reserved
# Licensed under the LGPL
# suggestions for improvement and bug fixes welcome at https://bitbucket.org/fubar/galaxytoolfactory/wiki/Hom... | nturaga/tools-iuc | tools/tool_factory_2/rgToolFactory2.py | Python | mit | 43,772 | [
"Galaxy"
] | 1f85dd13110cdf22f4feadfab375e02de6de14358b5737f63720fcad4da8cae1 |
#!/usr/bin/env python
__author__ = 'Mike McCann'
__copyright__ = '2013'
__license__ = 'GPL v3'
__contact__ = 'mccann at mbari.org'
__doc__ = '''
Master loader for all August 2013 SIMZ activities.
Mike McCann
MBARI 13 August
@var __date__: Date of last svn commit
@undocumented: __doc__ parser
@status: produ... | stoqs/stoqs | stoqs/loaders/MolecularEcology/loadSIMZ_aug2013.py | Python | gpl-3.0 | 6,720 | [
"NetCDF"
] | 017601b3de1e98e098f2b3fc5c62868fabc72183518e4ca687a7ca4ec05ff9a0 |
from ase import Atoms
from gpaw import GPAW
a = 4.5
H = Atoms('H', [(a / 2, a / 2, a / 2)],
pbc=0,
cell=(a, a, a))
calc = GPAW(nbands=1, h=0.2, charge=1)
H.set_calculator(calc)
print H.get_potential_energy() + calc.get_reference_energy()
assert abs(H.get_potential_energy() + calc.get_reference_ener... | robwarm/gpaw-symm | gpaw/test/proton.py | Python | gpl-3.0 | 334 | [
"ASE",
"GPAW"
] | 2f855adc49e8ea0034740a68af4ac432edbca4d079931ab8335f8a50cf6bcfa4 |
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simulation Environment ... | Chuban/moose | python/MooseDocs/common/moose_docs_import.py | Python | lgpl-2.1 | 5,311 | [
"MOOSE"
] | c25dece2d9e5aa660dfce950ccc9f81c2601654eaf33c2a71949df7fbc1f464b |
# Copyright 2013-2020 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):
"""Methods for microarray analysis that take basic data types such ... | iulian787/spack | var/spack/repos/builtin/packages/r-aroma-light/package.py | Python | lgpl-2.1 | 957 | [
"Bioconductor"
] | d42fce4e0ec318207362524d5f1d4691e186619681dd1bb41b238d485b07b907 |
#!/usr/bin/env python2
# Copyright (C) 2016
# Max Planck Institute for Polymer Research
#
# 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 ver... | fedepad/espressopp | examples/adress/fadress_tetraliquid/adress.py | Python | gpl-3.0 | 8,385 | [
"ESPResSo"
] | 1d33362efaaed15e8501a6cab2851fdfd52474dc065d53156be3e7dc5b8556ce |
from ase import Atoms
from gpaw import GPAW, FermiDirac, Mixer
#from gpaw.xc.noncolinear import NonColinearLDA, NonColinearLCAOEigensolver, \
# NonColinearMixer
h = Atoms('H', magmoms=[1])
h.center(vacuum=2)
xc = 'LDA'
c = GPAW(txt='c.txt',
mode='lcao',
basis='dz(dzp)',
#setups='ncpp',
... | robwarm/gpaw-symm | gpaw/test/colinear.py | Python | gpl-3.0 | 554 | [
"ASE",
"GPAW"
] | d67f6a61b12b9cf4f8907edc086ba953ade876b4ab89eec4690960af15e0f099 |
from setuptools import setup
def readme():
with open('README.rst') as f:
return f.read()
setup(name='dimerizer',
version='1.0.1',
description='The dimerizer script for Dimer simulations in Gromacs',
long_description=readme(),
classifiers=[
'Development Status :: 4 - Beta',
... | marckn/dimerizer | setup.py | Python | gpl-3.0 | 936 | [
"Gromacs"
] | 031bce881d0ad83c7f439fab0793ef5f2620413c09658f68cf3d38fee268ac23 |
import numpy as np
import ase
from ase.parallel import paropen
cfg_default_fields = np.array( [ 'positions', 'momenta', 'numbers', 'magmoms' ] )
def write_cfg(f, a):
"""Write atomic configuration to a CFG-file (native AtomEye format).
See: http://mt.seas.upenn.edu/Archive/Graphics/A/
"""
if isin... | suttond/MODOI | ase/io/cfg.py | Python | lgpl-3.0 | 7,319 | [
"ASE"
] | 3004568cfc8ab4464b557f2df4be538abe509eb3a39051d5fc0b7c49aed8e705 |
#!/usr/bin/env python
#
# Restriction Analysis Libraries.
# Copyright (C) 2004. Frederic Sohm.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
import re
import itertools
from Bio.Restri... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Restriction/PrintFormat.py | Python | gpl-2.0 | 13,734 | [
"Biopython"
] | 011219f3c51b66e49a5ff2b5bf33016b5bc6034e0aea9901d174d9b2b389ffd6 |
def agts(queue):
queue.add('testsuite.agts.py', ncpus=8, walltime=30)
if __name__ == '__main__':
# Run test suite
import gpaw.test.test
import os
assert not os.path.isfile('failed-tests.txt')
| qsnake/gpaw | gpaw/test/big/miscellaneous/testsuite.agts.py | Python | gpl-3.0 | 213 | [
"GPAW"
] | 146f28e63f21dff3ca404b2d7ab33477743408429ed68f3c9cb28a5cc3dad380 |
import gtk
from math import sqrt
from gettext import gettext as _
import numpy as np
from ase.gui.widgets import pack, Help
class Repeat(gtk.Window):
def __init__(self, gui):
gtk.Window.__init__(self)
self.set_title(_('Repeat'))
vbox = gtk.VBox()
pack(vbox, gtk.Label(_('Repeat at... | grhawk/ASE | tools/ase/gui/repeat.py | Python | gpl-2.0 | 1,309 | [
"ASE"
] | df7d014cf5df0e0731115d9e5ee31b46e278534a27e740cfc6ef1b1967ebdb1f |
"""
test views
"""
import datetime
import json
import re
import pytz
import ddt
from mock import patch, MagicMock
from nose.plugins.attrib import attr
from capa.tests.response_xml_factory import StringResponseXMLFactory
from courseware.courses import get_course_by_id # pyline: disable=import-error
from courseware.fie... | xuxiao19910803/edx-platform | lms/djangoapps/ccx/tests/test_views.py | Python | agpl-3.0 | 25,518 | [
"VisIt"
] | 96e34fa4f66067932bc04aefb5eb90cbab81a75279e7e53c9bfb54d7bc2f8057 |
# -*- 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_bak.py | Python | agpl-3.0 | 48,577 | [
"VisIt"
] | 916dea28797e09de97997bbe247db55bef2a6c371b470bcaf227dfe6034a1c6d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# __init__ - [insert a few words of module description on this line]
# Copyright (C) 2003-2011 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms o... | heromod/migrid | mig/grsfs-fuse/fs/core/network/rpc/__init__.py | Python | gpl-2.0 | 4,953 | [
"Brian"
] | 53d21711a83fa0fc691f01a0ebcb80002fe18967eefa938b9f57be212265585b |
#!/usr/bin/env python2
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# 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, eit... | kkreis/espressopp | examples/lattice_boltzmann/lb_md_coupling.py | Python | gpl-3.0 | 2,698 | [
"ESPResSo"
] | 3c4d8d5770134de58ef3236cb56b87f90f4dadec34536e5f6b1e45095ceffd6a |
#!/usr/bin/env
"""
ncutilities.py
Using Anaconda packaged Python
"""
import datetime
import numpy as np
from netCDF4 import Dataset
#user defined
import constants as constants
__author__ = 'Shaun Bell'
__email__ = 'shaun.bell@noaa.gov'
__created__ = datetime.datetime(2013, 12, 20)
__modified__ = datetim... | jeepsterboy/waveletanalysis | utilities/ncutilities.py | Python | mit | 3,214 | [
"NetCDF"
] | 1a9bec604dc29d21e33ec2169f0ab105fafc9f44a097af4ded11726db8871c88 |
#!/usr/bin/python
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Ansible is distributed... | bjolivot/ansible | lib/ansible/modules/files/xattr.py | Python | gpl-3.0 | 6,744 | [
"Brian"
] | 1cb8d4d92e0a9ab6853157229523e2cb22fbfd6640ddedd12a6d03a08cb40314 |
import django_databrowse
from django.contrib.staticfiles.urls import staticfiles_urlpatterns
from django.conf import settings
from django.conf.urls import include, url, patterns
from django.conf.urls.static import static
from django.contrib import admin
from django.contrib.auth.decorators import login_required
from dj... | botswana-harvard/bcvp | bcvp/urls.py | Python | gpl-2.0 | 2,684 | [
"VisIt"
] | ff38b178454710a0d33e44b6e5e89b341be0ddea066da2748da069e03b368082 |
# 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/management/commands/lock_expired.py | Python | gpl-3.0 | 2,021 | [
"Brian"
] | 234277bc87ea5b25b397e1a830535aa98de3ea3626efb5397e0211559ba3627c |
#!/usr/bin/env python3
"""
Copyright 2021 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester is free software: you can redistribute it and/or modify
it under the terms of the GNU Affero General Public License as published by
the Free Software Foundation, either version 3 ... | pwillworth/galaxyharvester | html/ghObjects.py | Python | gpl-3.0 | 40,375 | [
"Galaxy"
] | 5b78538a4bced89bb13429d892981ac8a53d1e190cee9d12fc0c1db31f20aff7 |
#!/usr/bin/env python
"""
Reads a list of intervals and a maf. Produces a new maf containing the
blocks or parts of blocks in the original that overlapped the intervals.
If a MAF file, not UID, is provided the MAF file is indexed before being processed.
NOTE: If two intervals overlap the same block it will be writte... | volpino/Yeps-EURAC | tools/maf/interval2maf.py | Python | mit | 6,159 | [
"Galaxy"
] | 89be7bb7928f354e3abc95bb619bdd2a9595649614498f070da7fa3b12717df4 |
# -*- coding: utf-8 -*-
# Copyright (C) 2010-2012, eskerda <eskerda@gmail.com>
# Distributed under the AGPL license, see LICENSE.txt
import json
import re
from lxml import html
from lxml import etree
from .base import BikeShareSystem, BikeShareStation
from . import utils
__all__ = ['BiciPalma']
COOKIE_URL = "http:... | javnik36/pybikes | pybikes/bicipalma.py | Python | lgpl-3.0 | 2,494 | [
"VisIt"
] | 0893a42b022be41c1c8bde073eb8b8dedde69f153f01dee05ec84c1b0c179722 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforge/simulation/neuron/hocmodbuilders/hocbuilder_cell.py | Python | bsd-2-clause | 4,743 | [
"NEURON"
] | 5a2e9bfd4bc068df49e26523d83ef890197bd8d7f6d328f5eeb821384842f3b3 |
# -*- coding: utf-8 -*-
"""
=====================
Statistical inference
=====================
Here we will briefly cover multiple concepts of inferential statistics in an
introductory manner, and demonstrate how to use some MNE statistical functions.
.. contents:: Topics
:local:
:depth: 3
"""
# Authors: Eric ... | mne-tools/mne-tools.github.io | 0.16/_downloads/plot_background_statistics.py | Python | bsd-3-clause | 28,636 | [
"Gaussian"
] | 974a7a991c1c01e564a8b5165046eaf4e81f593b3ebbdaf02e8c25800c231f92 |
#-------------------------------------------------------------------------------
# Name: orca_hess
# Purpose: Tests for opan.hess.OrcaHess
#
# Author: Brian Skinn
# bskinn@alum.mit.edu
#
# Created: 12 Mar 2016
# Copyright: (c) Brian Skinn 2016
# License: The MIT License; see "li... | bskinn/opan | opan/test/orca_hess.py | Python | mit | 69,843 | [
"Brian",
"ORCA"
] | 597860a3491e62ca1d11e3089cfb79b699b776c4631dd0473e1ab79c5e6f9dbe |
# -*- coding: utf-8 -*-
"""Mayavi/traits GUI visualization elements."""
# Authors: Christian Brodbeck <christianbrodbeck@nyu.edu>
#
# License: BSD (3-clause)
import numpy as np
from mayavi.mlab import pipeline, text3d
from mayavi.modules.glyph import Glyph
from mayavi.modules.surface import Surface
from mayavi.sourc... | teonlamont/mne-python | mne/gui/_viewer.py | Python | bsd-3-clause | 21,459 | [
"Mayavi"
] | 09d4fbc6adcf9434e5a7626345525301d929fce3e606d86ae0bac2b7ed9698e6 |
# -*- coding: utf-8 -*-
"""
Mathematical operations that generalize many operations from the standard math
and cmath modules so that they also track first and second derivatives.
The basic philosophy of order of type-operations is this:
A. Is X from the ADF class or subclass?
1. Yes - Perform automatic differentia... | tisimst/ad | ad/admath/admath.py | Python | bsd-3-clause | 46,933 | [
"ADF"
] | e386ebebf18c02ced5a13f626f51bf754601645ff4963cade01d43de961d2624 |
""" Main class for doing consistency checks, between files in:
- File Catalog
- TransformationSystem
Should be extended to include the Storage (in DIRAC)
"""
import six
import os
import time
import sys
import re
import errno
import DIRAC
from DIRAC import S_OK, S_ERROR, gLogger
from DIRAC.DataManagementSy... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/Client/ConsistencyInspector.py | Python | gpl-3.0 | 31,502 | [
"DIRAC"
] | f8e409443932bca5703e749adbbcd0622bfd5da5c4e8b008f1a05dbb6e43b5be |
from binary_tree_prototype import BinaryTreeNode
from binary_tree_utils import generate_postorder
# @include
# We use stack and previous node pointer to simulate postorder traversal.
def postorder_traversal(tree):
if not tree: # Empty tree.
return []
path_stack, prev, postorder_sequence = [tree], No... | meisamhe/GPLshared | Programming/MPI — AMath 483 583, Spring 2013 1.0 documentation_files/binary_tree_postorder_traversal_iterative.py | Python | gpl-3.0 | 1,744 | [
"VisIt"
] | b98e3c88632e96723b480929e5cadb10f7f4334e8c4fc398e4b5f41c2ab5caac |
#!/usr/bin/env python3
"""
Author: Kartamyshev A.I. (Darth Feiwante)
"""
def carrier_mobility(calc_init=(), calc_deform_x=(), calc_deform_y=(),
vbm=1, vbm_point=0, cbm=2, cbm_point=0,
deform_x=(), n_points_x=2, deform_y=(), n_points_y=2,
temperature_ra... | dimonaks/siman | siman/properties_2d.py | Python | gpl-2.0 | 22,880 | [
"VASP",
"pymatgen"
] | 23db94916bea8dc09849cfae3f5cf928365b3bdbf7cd0b78d9e1f9f7d5a5e050 |
from baseneuron import BaseNeuron
import numpy as np
import pycuda.gpuarray as garray
from pycuda.tools import dtype_to_ctype
import pycuda.driver as cuda
from pycuda.compiler import SourceModule
from neurokernel.LPU.utils.simpleio import *
cuda_src = """
// %(type)s and %(nneu)d must be replaced using Python string... | cerrno/neurokernel | neurokernel/LPU/neurons/LeakyIAF.py | Python | bsd-3-clause | 11,929 | [
"NEURON"
] | 652c880076e1929893bcdb2471617747af14112aa79c43d3bcf973e4e4d8eb7f |
''' -- imports from installed packages -- '''
import json
import datetime
''' -- imports from django -- '''
from django.shortcuts import render_to_response, render
from django.template import RequestContext
from django.template import Context
from django.template.defaultfilters import slugify
from django.core.urlresol... | olympian94/gstudio | gnowsys-ndf/gnowsys_ndf/ndf/views/forum.py | Python | agpl-3.0 | 41,404 | [
"VisIt"
] | 35df9994848eb66629ea144da3e61214abb5fca91502233bd1ee8814c2f0e88c |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | rmcgibbo/psi4public | psi4/driver/driver_util.py | Python | lgpl-3.0 | 10,595 | [
"Psi4"
] | 4c8a7a06a7188f65b771eabe29a192f0aa939963d499c6fac4a4c26a534cf4e2 |
#Copyright 2013 Thomas A Caswell
#tcaswell@uchicago.edu
#http://jfi.uchicago.edu/~tcaswell
#
#This program is free software; you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation; either version 3 of the License, or (at
#your option) an... | nkeim/trackpy | trackpy/identification.py | Python | gpl-3.0 | 9,989 | [
"Gaussian"
] | d18becd1e5ef2dc749912b5b0f3dc71fa95a8f2359bf14da5e2a93008e221fd3 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
r""" A JSON data encoder and decoder.
This Python module implements the JSON (http://json.org/) data
encoding format; a subset of ECMAScript (aka JavaScript) for encoding
primitive data types (numbers, strings, booleans, lists, and
associative arrays) in a language-n... | tanz-sullamora/angular-i18n | tools/demjson.py | Python | mit | 87,957 | [
"CDK"
] | efd6680c71e0c92381d2432d2bb32fb632bc6a3494325eea4a76bbb6ca0d889a |
from random import random
from opc.utils.prof import timefunc
# implementation of a linear feedback shift register generator that gives us
# n-bits of pseudo-random values, completing the entire sequence before
# repeating.
# polynomials required to calculate a n-bit lsfr. Higher bits are
# available, just not inclu... | slobberchops/rop | art/utils/lfsr.py | Python | gpl-3.0 | 4,131 | [
"VisIt"
] | 09da2580457bd7f1124afad469592e8b219f30516017043da10a19fb6603cda5 |
#!/usr/bin/env python
import vtk
from vtk.util.misc import vtkGetDataRoot
# create planes
# Create the RenderWindow, Renderer
#
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer( ren )
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# create pipeline
#
pl3d = vtk.vtkPLOT3... | naucoin/VTKSlicerWidgets | Graphics/Testing/Python/glyphComb.py | Python | bsd-3-clause | 1,241 | [
"VTK"
] | 5b9410f267c2e9b658ecf4dd2826c6b0b7a6b97b504e5f4614b50355e83b04db |
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are ... | eleftherioszisis/NeuroM | neurom/view/dendrogram.py | Python | bsd-3-clause | 7,275 | [
"NEURON"
] | 724a4c6ee83d4d6b305ee8a26700e1c71d10e467206b3f67d333043da0906c6e |
"""
Views for user API
"""
from django.shortcuts import redirect
from django.utils import dateparse
from rest_framework import generics, views
from rest_framework.decorators import api_view
from rest_framework.response import Response
from opaque_keys.edx.keys import UsageKey
from opaque_keys import InvalidKeyError
... | analyseuc3m/ANALYSE-v1 | lms/djangoapps/mobile_api/users/views.py | Python | agpl-3.0 | 11,095 | [
"VisIt"
] | b383ba543c86982d55c8e34eb3163a62b3fea2037ff4c6b336530f70dd491aac |
"""
Django module container for classes and operations related to the "Course Module" content type
"""
import logging
from cStringIO import StringIO
from math import exp
from lxml import etree
from path import path # NOTE (THK): Only used for detecting presence of syllabus
import requests
from datetime import datetime... | antonve/s4-project-mooc | common/lib/xmodule/xmodule/course_module.py | Python | agpl-3.0 | 58,585 | [
"VisIt"
] | 7ea5b6e08e9ce8903d9b549f59e885ed790f6d187d574e501aa16cc612fa2c92 |
# Copyright (C) 2012,2013,2017(H)
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
# Copyright (C) 2019
# Max Planck Computing and Data Facility
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free so... | espressopp/espressopp | src/standard_system/Default.py | Python | gpl-3.0 | 2,624 | [
"ESPResSo"
] | c57ea8b6b319fcd693c48c318c97914a0e6b56e5e7ae11a6cb254ee26e9db0d0 |
# husk:
# Exit*2? remove pylab.show()
# close button
# DFT
# ADOS
# grey-out stuff after one second: vmd, rasmol, ...
# Show with ....
# rasmol: set same rotation as ag
# Graphs: save, Python, 3D
# start from python (interactive mode?)
# ascii-art option (colored)|
# option -o (output) and -f (force overwrite)
# surfa... | grhawk/ASE | tools/ase/gui/gui.py | Python | gpl-2.0 | 48,937 | [
"ASE",
"Avogadro",
"CASTEP",
"CRYSTAL",
"FHI-aims",
"GPAW",
"NetCDF",
"RasMol",
"TURBOMOLE",
"VASP",
"VMD",
"WIEN2k",
"exciting"
] | 0da84b2d8067f0fac5d28881cedb404bfacb66604950bb91104383215abd4ed9 |
from jaspyx.visitor import BaseVisitor
class FuncType(BaseVisitor):
def func_type(self, arg):
self.output('typeof ')
self.visit(arg)
| iksteen/jaspyx | jaspyx/visitor/func_type.py | Python | mit | 155 | [
"VisIt"
] | c68a43fe24f71c245fd3fcbb90c8fb7219b8d9b1bfd7c18a5fd66360aabcd29e |
'''
This module performs the return type inference, according to symbolic types,
It then reorders function declarations according to the return type deps.
* type_all generates a node -> type binding
'''
from pythran.analyses import (LazynessAnalysis, StrictAliases, YieldPoints,
Loc... | hainm/pythran | pythran/types/types.py | Python | bsd-3-clause | 24,606 | [
"VisIt"
] | fe743e02e4e9b2168c331754be19eca5abd9c6ed2f359a3e61abf856db00b5d7 |
"""test_smooth - test the smoothing module
CellProfiler is distributed under the GNU General Public License,
but this file is licensed under the more permissive BSD license.
See the accompanying file LICENSE for details.
Copyright (c) 2003-2009 Massachusetts Institute of Technology
Copyright (c) 2009-2015 Broad Insti... | LeeKamentsky/CellProfiler | cellprofiler/cpmath/tests/test_smooth.py | Python | gpl-2.0 | 4,278 | [
"Gaussian"
] | 7d3911aa1f971c9c5dfba88abb9a6ce4c80e91a9d161a19f148af4dccfe04611 |
# Copyright (c) 2005 Gavin E. Crooks <gec@threeplusone.com>
#
# This software is distributed under the MIT Open Source License.
# <http://www.opensource.org/licenses/mit-license.html>
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation... | NarlikarLab/DIVERSITY | weblogoMod/corebio/seq_io/clustal_io.py | Python | gpl-3.0 | 7,981 | [
"BioPerl"
] | 3fc2f6eb10615a88d5cc404cf8d5cbe1f580dffbcab3c0748ac20062089292c8 |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import os, subprocess
import gobject
import dialog
from StringIO import StringIO
from zeroinstall import _
from zeroinstall.injector import model, selections, qdom
XMLNS_0COMPILE = 'http://zero-install.sourceforge.n... | timdiels/zeroinstall | zeroinstall/0launch-gui/compile.py | Python | lgpl-2.1 | 3,252 | [
"VisIt"
] | c758de31017c1feb5a0b28fa702453554824a590acfe23ef7cd5a0ac97da616b |
import pybel
from pybel import *
import copy_reg
import numpy as np
from openbabel import OBAtomAtomIter,OBTypeTable
from oddt.spatial import angle, angle_2v, dihedral
backend = 'ob'
# setup typetable to translate atom types
typetable = OBTypeTable()
typetable.SetFromType('INT')
typetable.SetToType('SYB')
# hash OB!
... | mwojcikowski/opendrugdiscovery | oddt/toolkits/ob.py | Python | bsd-3-clause | 11,677 | [
"Open Babel",
"Pybel"
] | f0a498eea8933b6a1bf25e2f0135b845030afe34942cf370c50b496bc8e6a844 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals, division, absolute_import
from datetime import timedelta, datetime
import pytest
from builtins import * # pylint: disable=unused-import, redefined-builtin
from flexget.manager import Session
from flexget.plugins.internal.api_tvmaze import APITVMaze, T... | oxc/Flexget | flexget/tests/test_tvmaze.py | Python | mit | 21,042 | [
"Firefly"
] | f80cb87ae2dca1c91e760a8cd4e89ea42f63987a18ead004cf17c5171e0aef91 |
import numpy as np
import theano as th
import theano.tensor as tt
import theano.tensor.signal.conv as sigconv
from .layer import Layer
float_x = th.config.floatX
# ############################## Input Layer ##################################
class InputLayer(Layer):
def __init__(self, inpt, img_sz, num_maps=1,... | nagyistoce/theanet | theanet/layer/inlayers.py | Python | apache-2.0 | 5,844 | [
"Gaussian"
] | b0c4a38d50f36bdf659d45cee5695f66395e5b5e52dae75363a0e60354ef889f |
import os
import re
import shutil
import sys
if sys.version_info[:2] < (2, 6):
sys.exit('virtualenv requires Python 2.6 or higher.')
try:
from setuptools import setup
from setuptools.command.test import test as TestCommand
class PyTest(TestCommand):
user_options = [('pytest-args=', 'a', "Argu... | Leonnash21/flask_heroku | setup.py | Python | mit | 4,311 | [
"Brian"
] | 951eea6ad8fa4d5484b63d48dbb5d0ff29b07936a41c474d2dd2cbef9398525a |
"""
Routines and Frameworks for intelligent integration of the correlation function,
to obtain eg. projected and angular correlations functions.
"""
import numpy as np
from scipy.interpolate import InterpolatedUnivariateSpline as _spline
from scipy.integrate import simps
from .halo_model import HaloModel
from hmf impo... | steven-murray/halomod | src/halomod/integrate_corr.py | Python | mit | 17,478 | [
"Galaxy"
] | 9249d8bb068e2ecf2d718ae9b0f29094880435fc9cc036c1bc9831f474ad5055 |
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