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# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/plugins/alerts/lib/db.py | Python | gpl-2.0 | 2,872 | [
"Brian"
] | 505ad17275fe824ac8ee912f75d4d57562c65d652ee88bf97ffac80423638ce4 |
"""params_circuit.py: Summarizes parameters of neurons and the network in
dictionary. Each parameter set implements two functions. One specifying
all default parameter and one calculating the parameter that can be
derived from the default parameter. The default parameter will be used
to create a hash when saving result... | INM-6/neural_network_meanfield | params_circuit.py | Python | gpl-3.0 | 6,324 | [
"Gaussian"
] | 8e1a23b95d1af367f687c55fa0b84a7339f3279f150034c05ec4462c41673eed |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import time
##############################################
# Configuration, please edit
##############################################
# Data about this site
BLOG_AUTHOR = "Your Name"
BLOG_TITLE = "Demo Site"
# This is the main URL for your site. It wi... | servalproject/nikola | tests/data/translated_titles/conf.py | Python | mit | 13,774 | [
"VisIt"
] | 6cba3acc3601d00edb738c6cbc9ad2aa69ddde40050666a9a31db62ffcc36e5d |
from django.shortcuts import render
from django.views.generic import TemplateView, View
from django.http import HttpResponse
from django.views.decorators.cache import cache_page
from django.views.decorators.csrf import csrf_exempt
from django.conf import settings
from django.db.models import Count, Q, Prefetch
from c... | cmunk/protwis | construct/views.py | Python | apache-2.0 | 131,498 | [
"CRYSTAL"
] | 22e327310e93d5c71ff3fdb52e6f61ab490a7322e07acbc20744fd8fb717f793 |
import numpy as np
from ase import Atom, Atoms
from gpaw import GPAW, Mixer, RMM_DIIS
from gpaw.test import equal
a = 4.0
n = 20
d = 1.0
x = d / 3**0.5
atoms = Atoms([Atom('C', (0.0, 0.0, 0.0)),
Atom('H', (x, x, x)),
Atom('H', (-x, -x, x)),
Atom('H', (x, -x, -x)),
... | robwarm/gpaw-symm | gpaw/test/blocked_rmm_diis.py | Python | gpl-3.0 | 888 | [
"ASE",
"GPAW"
] | 849f4926720a997c485a1fc5578a2448a7b00432d821cdacb7c94995afba4b91 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | fweik/espresso | testsuite/python/observable_cylindrical.py | Python | gpl-3.0 | 10,523 | [
"ESPResSo"
] | 80e5b4d2675cecdca6e3a5956f96896ab8c3f9c41bd651e8e6e306cfb8c2a5ea |
#!/usr/bin/python
# Copyright 2003-2016 Gentoo Foundation
# Distributed under the terms of the GNU General Public License v2
from __future__ import print_function
__author__ = "Thomas de Grenier de Latour (tgl), " + \
"modular re-write by: Brian Dolbec (dol-sen)"
__email__ = "degrenier@easyconnect.fr, " + \
"bri... | zmedico/gentoolkit | pym/gentoolkit/eclean/cli.py | Python | gpl-2.0 | 18,562 | [
"Brian"
] | f3c76bf3efb5b69521b369af8251110fb17a898de96023afe337ed46be3d7927 |
from collections import Sequence
from distutils.version import LooseVersion
import logging
import warnings
import sys
import os
from os import path as op
import inspect
from functools import wraps
import mayavi
from mayavi import mlab
from mayavi.filters.api import Threshold
import numpy as np
import nibabel as nib
fr... | mwaskom/PySurfer | surfer/utils.py | Python | bsd-3-clause | 25,506 | [
"Mayavi"
] | e3ee74187b57007508300da838c7cf71ee3f804fbd4cfa207ad0412356b1c373 |
#!/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.
#
"""
Usage:
=====
>>> from Rana.fts imp... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Restriction/__init__.py | Python | gpl-2.0 | 8,744 | [
"Biopython"
] | bee9a3ff2653e27ae9375cdc2aabda6271e37319cf88436b5ea89e20d50e6300 |
from django.contrib.postgres.aggregates import ArrayAgg
from django.conf import settings
from django.http import JsonResponse
from django.shortcuts import render, redirect
from django.views.decorators.csrf import csrf_exempt
#from common.views import AbsTargetSelection
from common.views import AbsTargetSelectio... | protwis/protwis | phylogenetic_trees/views.py | Python | apache-2.0 | 21,508 | [
"CRYSTAL"
] | 3fcda4d13494071054a82d9e6c0a08aac1bc580931228b47a04fc99f29798a4f |
"""
Set of programs and tools to read the outputs from RH, 1.5D version
"""
import os
import warnings
import datetime
import numpy as np
import xarray as xr
import h5py
import netCDF4
from io import StringIO
from astropy import units
class Rh15dout:
"""
Class to load and manipulate output from RH 1.5D.
""... | ITA-Solar/helita | helita/sim/rh15d.py | Python | bsd-3-clause | 31,586 | [
"NetCDF"
] | 0b5ece4ef8a2416a95edecae16009a2bca35eac3620b2a88303743a0c912effa |
"""Bayesian Gaussian Mixture Models and
Dirichlet Process Gaussian Mixture Models"""
from __future__ import print_function
# Author: Alexandre Passos (alexandre.tp@gmail.com)
# Bertrand Thirion <bertrand.thirion@inria.fr>
#
# Based on mixture.py by:
# Ron Weiss <ronweiss@gmail.com>
# Fabian Ped... | treycausey/scikit-learn | sklearn/mixture/dpgmm.py | Python | bsd-3-clause | 31,090 | [
"Gaussian"
] | 38adeba6945cf052c7cb340abc8affd5d1876c8f8eb1aea12b197cfa6cef534a |
import bs4
from typing import List, Dict
from collections import namedtuple
from difflib import SequenceMatcher
from .logger import Logger
from .gallery import GenericGallery
from .request_managers import ex_request_manager, chaika_request_manager
ChaikaResult = namedtuple("ChaikaResult", "url title")
class Search(Lo... | seanegoodwin/PandaViewer | PandaViewer/search.py | Python | gpl-3.0 | 5,215 | [
"MOE"
] | 4a9fd25a277db53fc805625041183a3fe885a1a9069fcf32f77a46e699a18ffa |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/item_title | openlp/core/ui/themelayoutdialog.py | Python | gpl-2.0 | 4,397 | [
"Brian"
] | d788ba69121933da54e097509f01d4fa3600b3e9a0c60d969b468b6b38124317 |
# Licensed under an MIT open source license - see LICENSE
import numpy as np
import matplotlib.pyplot as p
import scipy.ndimage as nd
from scipy.stats import lognorm
from skimage.morphology import remove_small_objects, medial_axis
from astropy.io import fits
from astropy.table import Table, Column
from astropy import ... | e-koch/FilFinder | fil_finder/filfinder2D.py | Python | mit | 58,807 | [
"Gaussian"
] | 7f14db561d3a674ad4b59d92ea09ffb4cab9f62d3cb894671ea6c8e7d6780c38 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-ban-site
# Author : Stuart Paterson
########################################################################
"""
Remove Site from Active mask for current Setup
Example:
$ dirac-admin-ban-site LCG.I... | DIRACGrid/DIRAC | src/DIRAC/Interfaces/scripts/dirac_admin_ban_site.py | Python | gpl-3.0 | 3,347 | [
"DIRAC"
] | d1a4491735803bc8fde3835d14e7008b724ca8cf55feb9d25b01f40326ded2f3 |
# Copyright (C) 2010-2014 CEA/DEN, EDF R&D
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This library ... | FedoraScientific/salome-paravis | test/VisuPrs/SWIG_scripts/B0.py | Python | lgpl-2.1 | 1,920 | [
"VTK"
] | c9b38e8ea1131bf70180245d44b316a55da123aafb10dd8abad321459979f3c6 |
##input: /Users/metagenomics/Documents/Databases/uniprot_tremble.dat or uniprot_sprot.dat
import sys
import os
from Bio import SeqIO
#import gzip
#This script uses biopython to get taxonomy from uniprot .dat file
'''
record.annotations record.letter_annotations
record.dbxrefs record.lower
record.d... | fandemonium/code | uniprot_dat.py | Python | mit | 914 | [
"Biopython"
] | cba4dc0a5b12a150d42a34537d0422b7dc531a4ff28b5ded82d60d95cf8396f8 |
#!/usr/bin/env python3
import math
import warnings
from abc import ABC, abstractmethod
from copy import deepcopy
import torch
from .. import settings
from ..distributions import MultivariateNormal, base_distributions
from ..module import Module
from ..utils.quadrature import GaussHermiteQuadrature1D
from ..utils.war... | jrg365/gpytorch | gpytorch/likelihoods/likelihood.py | Python | mit | 16,260 | [
"Gaussian"
] | 7aa3d5fc69a99d17cd1fde09705b84f257c583bbba5c561bf10eb5451f0fbcd7 |
# -*- coding: utf-8 -*-
############################################################################
# Copyright (C) 2010 by Nestor Aguirre #
# nfaguirre@imaff.cfmac.csic.es #
# ... | nfaguirrec/piamod | src/Crystal.py | Python | gpl-2.0 | 8,336 | [
"CRYSTAL"
] | c032d01113a35a98927c2c6fbdeeea3ce038195fb4e175b2ca182a168adbfeec |
# (C) 2016, Markus Wildi, wildi.markus@bluewin.ch
#
# 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, or (at your option)
# any later version.
#
# This program is distr... | RTS2/rts2 | scripts/u_point/transform/u_libnova.py | Python | lgpl-3.0 | 8,905 | [
"VisIt"
] | 2c4c8affa2b244c0fa92cc3804f12ef3434f2438c8aed26afadc1ac0eb8fefec |
from datetime import datetime, timedelta
import time
from dateutil.parser import parser
from django.core.cache import cache
import simplejson
from casexml.apps.case.models import CommCareCase
from corehq.apps.api.es import ReportXFormES, get_report_script_field
from pact.enums import PACT_DOMAIN
from pact.lib.quicksect... | SEL-Columbia/commcare-hq | custom/_legacy/pact/reports/chw_schedule.py | Python | bsd-3-clause | 10,412 | [
"VisIt"
] | defee02e47b04d4fdfcae0ba5c9c3acac2fc0b3b57c1a46385ccc431a00c0077 |
# author: brian dillmann
# for rscs
from context import Input
from context import Output
from context import Timer
from context import AnalogInput
import unittest
class test_device_simple(unittest.TestCase):
def test_naming_convention(self):
import RPi
RPi.GPIO.setmode(RPi.GPIO.BCM)
with self.assertRaises(Valu... | dillmann/rscs | test/devicetests/device_test.py | Python | mit | 685 | [
"Brian"
] | 39270de78ef46b00541fd3143e3854d1e60242d07e791cb06d421792230fd97b |
# encoding:utf-8
'''
Exemplo módulo pairwise2
Doc:
http://biopython.org/DIST/docs/api/Bio.pairwise2-module.html
'''
from Bio.pairwise2 import *
'''
alinhamento global
1 ponto para match (caractere igual)
nenhum ponto para mismatch ou gap
'''
print 'Alinhamentos globais:\n'
alignments = align.globalxx('ACCGT',... | marcoscastro/pybr11 | codigos/17_alinhamentos.py | Python | gpl-2.0 | 701 | [
"Biopython"
] | db609b0f5c732037d039a6e85ca211275eab9eb888b64041f5d1afa04fa0dec9 |
# -*- coding: utf-8 -*-
#
# Gpipe documentation build configuration file, created by
# sphinx-quickstart on Mon Jul 20 11:17:20 2009.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
#
# All... | CGATOxford/CGATPipelines | doc/conf.py | Python | mit | 11,285 | [
"pysam"
] | a8564059c69d6a8487e9d9780ab65012b874b4e66edc0314fc620294e893a079 |
from pprint import pprint
from dateutil.parser import parse
from arrow import Arrow
import requests
runi = lambda s: s.encode('cp850', errors='replace').decode('cp850')
BASE = 'https://graph.facebook.com/v2.0/'
DAYS = [
'monday',
'tuesday',
'wednesday',
'thursday',
'friday',
'saturday',
... | Mause/parkd | event_posts.py | Python | mit | 2,418 | [
"VisIt"
] | f2ebb2b752e1d86e5112d55f7dcdc9902919ddcb762495f73703bf4c7bddf429 |
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2007, 2012, 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 it... | smarr/GraalCompiler | mx.graal/sanitycheck.py | Python | gpl-2.0 | 19,705 | [
"VisIt"
] | ccf055dc3afc5fb028f1feddda76b4a3e0e08eea3eb41b3a247c8b4add7c7ab3 |
#
# Copyright (C) 2014 FreeIPA Contributors see COPYING for license
#
import random
import ctypes.util
import binascii
import struct
import six
from cryptography.hazmat.backends import default_backend
from cryptography.hazmat.primitives import serialization
from cryptography.hazmat.primitives.asymmetric import dsa, ... | encukou/freeipa | ipaserver/p11helper.py | Python | gpl-3.0 | 65,253 | [
"CRYSTAL"
] | c3be86b935d3e9f5f5d6b41590260af362c55c0a7bf84d52cd78a68385be53db |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# This module is also sponsored by E.T.A.I. (www.etai.fr)
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version... | ujenmr/ansible | lib/ansible/modules/cloud/vmware/vmware_guest.py | Python | gpl-3.0 | 134,383 | [
"VisIt"
] | 3b77c0b667edcf39841df0efa2a6d6b37eeab0accbddffcf14e9a62b8c347c30 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | jturney/psi4 | psi4/driver/procrouting/proc.py | Python | lgpl-3.0 | 202,348 | [
"Psi4"
] | 295a010c8dbc531cb405431fe72b5b0aa5a6f796d761a8eeabdc7c9a9b925fee |
from log import wl_log, add_log_file_handler, add_symlink
from random import choice
from selenium.common.exceptions import TimeoutException
from torutils import TorController
from visit import Visit
import common as cm
import os
import time
import utils as ut
class Crawler(object):
"""Provides methods to collect ... | pankajb64/webfp-crawler-phantomjs | tor-browser-crawler-webfp-paper/datacollection/crawler.py | Python | gpl-2.0 | 6,244 | [
"VisIt"
] | 760046b35649b420c0cff597b473d6388e4eb9bd96e2c3170ec997cad18e0fb3 |
#!/usr/bin/env python
"""HDSS fieldwork simulation, using openHDS"""
__email__ = "nicolas.maire@unibas.ch"
__status__ = "Alpha"
import json
import datetime
import os
import MySQLdb.cursors
import random
import numpy as np
import time
from matplotlib.path import Path
import argparse
import submission
import util
impo... | SwissTPH/openhds-sim | fieldwork_simulator.py | Python | gpl-2.0 | 27,757 | [
"VisIt"
] | 584cbd2af4c602aa97dc89be8504380925b9bc03694105d7ad264d79ade3dbf8 |
# -*- coding: utf-8 -*-
#
# hill_tononi_Vp.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 License,... | terhorstd/nest-simulator | topology/examples/hill_tononi_Vp.py | Python | gpl-2.0 | 36,473 | [
"Gaussian",
"NEURON"
] | 5647b510648c075d83c41b95e31bef2c9d4ebdeb8a3cf63706d5d84fb2026fab |
# Copyright (c) 2012 Spotify AB
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may not
# use this file except in compliance with the License. You may obtain a copy of
# the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, s... | samepage-labs/luigi | setup.py | Python | apache-2.0 | 3,014 | [
"VisIt"
] | 1a3afc2d08e3be2e840819d4cb4fe159d1912a155469324a7b724292bf0693d0 |
# Copyright 2012 OpenStack Foundation
# All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requ... | barnsnake351/neutron | neutron/tests/unit/agent/linux/test_ip_lib.py | Python | apache-2.0 | 49,793 | [
"Brian"
] | c6745bf1aff61170081a6126d7a2e6f02bcaf83ddc60895ac676b66d5a14cf9a |
import sys
sys.path.insert(1,"../../../")
import h2o
from tests import pyunit_utils
from h2o.estimators.glm import H2OGeneralizedLinearEstimator as glm
import numpy as np
# This test will generate synthetic GLM dataset. If given to a GLM model, it should be able to perform well with
# this dataset since the assumpti... | h2oai/h2o-3 | h2o-py/tests/testdir_algos/glm/pyunit_generate_synthetic_GLM_data.py | Python | apache-2.0 | 4,559 | [
"Gaussian"
] | e4b6ffe4298bd008dfc21e10b0a786afe28988e058424cbdeef9d03c4d403214 |
#!/usr/bin/env python
"""
Packages for descriptors.
Usage:
desc.py [options]
Options:
-h, --help Show this message and exit.
-i IFNAME Input file name. [default: in.params.desc]
-o OFNAME Output file name. [default: in.params.desc]
"""
from __future__ import print_function
from docopt import docopt
__a... | ryokbys/nap | nappy/nn/desc.py | Python | mit | 3,976 | [
"Gaussian"
] | e272781b3e908805b180aa4fd0b2e3fe2fc7b49363cc56ffed1b3aa057b12309 |
__author__ = 'Timotheus Kampik'
import sys
import random
# import and init pygame
import pygame
pygame.init()
window = pygame.display.set_mode((640, 480))
def draw():
# get random number of gaussian distribution with mean=window_width/2 and standard deviation=60
num = random.gauss(window.get_width()/2, 60)
... | TimKam/TheNatureOfCodePython | Introduction/Example_4_Gaussian/gaussian.py | Python | mit | 599 | [
"Gaussian"
] | b2a142d2d1894b36ec7998a6bab2ef3c150341790d6e2bbc05ff6630697b23ac |
#coding: utf8
from datetime import datetime, timedelta
from itertools import chain
import django
from django.db.models import Q
from django.core.urlresolvers import reverse
from django.contrib import messages
from django.template import RequestContext
from django.shortcuts import get_object_or_404, render_to_response... | dicos/geneticist | apps/patient/views.py | Python | gpl-3.0 | 14,516 | [
"VisIt"
] | 832255876be70902d7c9e191bae5aeeed51393bb6d138047bfeba292c3682c80 |
"""
simple, elegant templating
(part of web.py)
Template design:
Template string is split into tokens and the tokens are combined into nodes.
Parse tree is a nodelist. TextNode and ExpressionNode are simple nodes and
for-loop, if-loop etc are block nodes, which contain multiple child nodes.
Each node can emit some p... | lastr2d2/lastchat | src/lib/web/template.py | Python | gpl-2.0 | 47,974 | [
"VisIt"
] | a3eabb0108ecaa8ff8b43d5c85162fe77e8978a94df5742fda176a2c964a45ec |
#!/usr/bin/env python
#
# Engineering Calculator Actions
#
# An RPN calculator that supports numbers with SI scale factors and units.
# Imports {{{1
from __future__ import division
import operator
import math
import cmath
import random
from calculator import \
Command, Constant, UnaryOp, BinaryOp, BinaryIoOp, Numb... | KenKundert/ec0 | actions.py | Python | gpl-3.0 | 79,995 | [
"Avogadro"
] | 3c688a1d2eca5cdaa78f84a294dd77cdd0e31deb6af5e19951a9ca40dbe9fde9 |
# This demo illustrates how mtSet can be used for multi and single-trait set tests
# We consider a dataset of 192 samples and 3 flowering time phenotypes in A.thaliana from Atwell et al 2010 (Nature)
# Phenotypes were quantile-normalized to a gaussian distribution beforehand
# Here we consider 3 different models
# - m... | PMBio/mtSet | notebooks/arab_demo.py | Python | apache-2.0 | 6,963 | [
"Gaussian"
] | c2aa72bcf9fde89b478af2811a9fc889f0c9cffe3aefcf60bb54c8d6ff07e878 |
"""
State Space Analysis using the Kalman Filter
References
-----------
Durbin., J and Koopman, S.J. `Time Series Analysis by State Space Methods`.
Oxford, 2001.
Hamilton, J.D. `Time Series Analysis`. Princeton, 1994.
Notes
-----
This file follows Hamilton's notation pretty closely.
"""
from scipy import opt... | matthew-brett/draft-statsmodels | scikits/statsmodels/sandbox/tsa/kalmanf.py | Python | bsd-3-clause | 15,822 | [
"Gaussian"
] | fd2645187b15554aa635c485e7fda2013dc15a895dd3098ca6cc2fe33df7f154 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Author: Andrew Jewett (jewett.aij at g mail)
# http://www.chem.ucsb.edu/~sheagroup
# License: 3-clause BSD License (See LICENSE.TXT)
# Copyright (c) 2012, Regents of the University of California
# All rights reserved.
"""
ltemplify.py
The "ltemplify.py" script... | ramisetti/lammps | tools/moltemplate/moltemplate/ltemplify.py | Python | gpl-2.0 | 180,315 | [
"LAMMPS"
] | 20d283e1845fdb4db31a3690c2ee3a04d8344d1028b58050765fc2ae921a5169 |
from __future__ import division, print_function
import numpy as np
import os
from auxiliary import *
from scipy.integrate import odeint, ode
import matplotlib.pyplot as plt
from smatrix import compute_S_matrix, compute_S_matrix_fast, mean_poisson
from ttsolution import TTsolution
import sys
try:
xrange
except NameE... | aripekka/pytakagitaupin | takagitaupin.py | Python | mit | 8,086 | [
"CRYSTAL"
] | 92650c5e1509173a0a2e7f3c6e99d1892dfba8c990194c8524874ec61fe307d8 |
# (C) British Crown Copyright 2010 - 2016, Met Office
#
# This file is part of Iris.
#
# Iris 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 l... | davidnmurray/iris | lib/iris/fileformats/netcdf.py | Python | gpl-3.0 | 73,435 | [
"NetCDF"
] | 9472aa1ac0a88d9d2cf03cc7ace52012c1bfcebfbac042f64877dd8f8a5995fc |
import matplotlib.pyplot as plt
from gpaw import GPAW
calc = GPAW('ferro.gpw', txt=None)
ef = calc.get_fermi_level()
# Plot s, p, d projected LDOS:
for c in 'spd':
energies, ldos = calc.get_orbital_ldos(a=0, spin=0, angular=c, width=0.4)
plt.plot(energies - ef, ldos, label=c + '-up')
energies, ldos ... | robwarm/gpaw-symm | doc/exercises/dos/pdos.py | Python | gpl-3.0 | 459 | [
"GPAW"
] | fcdd5a9be960cc085f4ba9713fa63cb9efbec963f984421661a13c093eea4d6e |
# -*- coding: utf-8 -*-
# Copyright (C) Duncan Macleod (2014-2020)
#
# This file is part of GWpy.
#
# GWpy 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)... | gwpy/gwpy | gwpy/timeseries/tests/test_timeseries.py | Python | gpl-3.0 | 54,741 | [
"Gaussian"
] | dd815a264b5bf0bc84d81d1a0914bc28e713b547312c96db92e7b2c94e5a9a28 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2004-2007 Donald N. Allingham
# Copyright (C) 2010 Brian G. Matherly
# Copyright (C) 2014 Paul Franklin
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as publ... | prculley/gramps | gramps/gen/display/name.py | Python | gpl-2.0 | 46,036 | [
"Brian"
] | 6c20e1ba5fca9e4ebb02174252d099922520cd00520f16419ac39f6284c777e8 |
"""
Views related to the Custom Courses feature.
"""
import csv
import datetime
import functools
import json
import logging
import pytz
from copy import deepcopy
from cStringIO import StringIO
from django.conf import settings
from django.core.urlresolvers import reverse
from django.http import (
HttpResponse,
... | fintech-circle/edx-platform | lms/djangoapps/ccx/views.py | Python | agpl-3.0 | 22,571 | [
"VisIt"
] | 8a0d14dbf165cb4e6f300d242c905e29a3573c0a495168c2434dd54fa3dce08b |
#!/usr/bin/env python
# Copyright (c) 2009, South African Astronomical Observatory (SAAO) #
# All rights reserved. #
"""
SPECSENS calulates the calibration curve given an observation, a standard star,
and the extinction curve for the site. The task assumes a 1... | saltastro/pysalt | saltspec/specsens.py | Python | bsd-3-clause | 6,366 | [
"Gaussian"
] | aee4a75c73c0c818533358f22c1b18606aec571658233b0de0b9dd6dad3569f9 |
import logging
from edx_rest_api_client.client import EdxRestApiClient
from acceptance_tests import config
from acceptance_tests.pages import LMSLoginPage
log = logging.getLogger(__name__)
class LoginMixin:
"""Mixin used for log in through LMS login page."""
def setUp(self):
super().setUp()
... | edx/credentials | acceptance_tests/e2e/mixins.py | Python | agpl-3.0 | 1,690 | [
"VisIt"
] | b1fb1c94e0e25254e81befe9f0c67f8ad34d6724f123b05cabcfa0be9baff452 |
# -*- coding: utf-8 -*-
# @Author: Zachary Priddy
# @Date: 2016-04-26 23:06:59
# @Last Modified by: Zachary Priddy
# @Last Modified time: 2016-10-12 23:14:47
import logging
from core.models.app import App
from core.models.command import Command as ffCommand
class App(App):
METADATA = {
'title' : 'Firefl... | zpriddy/Firefly | Firefly/apps/ffAdvancedLighting/lux.py | Python | apache-2.0 | 5,780 | [
"Firefly"
] | 1a069b2e63328acc25f2aa6d0a5d4a0490bfb2a559cb79fdb6c1fd530f62eedb |
#!/usr/bin/env python
#
# $File: demoFunc.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribute i... | BoPeng/simuPOP | docs/demoFunc.py | Python | gpl-2.0 | 1,483 | [
"VisIt"
] | cf36f61c4ac9279452c269d0c22f2ed1620309e5360dcc62f90350fba1d41a59 |
import argparse
import itertools
import logging
import os
import re
import simplejson as json
from Bio.PDB.PDBParser import PDBParser
from Bio.PDB import NeighborSearch
from config import PDB_RESIDUE_TYPES_BY_RESIDUE
LEVEL_MAP = {
'A': 'atom',
'R': 'residue',
'C': 'chain'
}
# MATCHES PDB ACCESSIONS
# E... | harryjubb/pdb_interactions | determine_interactions.py | Python | mit | 10,147 | [
"Biopython"
] | 4070b8c7815dfc4c23e56c5a7a62c4caf507296cd5dbd962e4228e322f2642aa |
#!/usr/bin/env python
#
# Copyright 2017 Phedorabot
#
# 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... | Phedorabot/phedorabot-python-sdk | phedorabot/onetime.py | Python | apache-2.0 | 9,192 | [
"VisIt"
] | af27226f477d8a84ffa6962c72e5d1c298da431b4bba3fac49061fb6ae481980 |
# Copyright (c) 2020 PaddlePaddle 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 app... | PaddlePaddle/Paddle | python/paddle/fluid/dygraph/dygraph_to_static/return_transformer.py | Python | apache-2.0 | 18,556 | [
"VisIt"
] | 9cb9c35cb019b5c42f237449da61dd733612e8fea33826ce0a54d75412838278 |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Module to support the loading of a NetCDF file into an Iris cube.
See also: `netCDF4 python <http://code.google.com/p/netc... | pp-mo/iris | lib/iris/fileformats/netcdf.py | Python | lgpl-3.0 | 100,575 | [
"NetCDF"
] | 83a7eb76353d541fd15b21d01a981faa598a8a9f2c688baae0e8920b2653ec2a |
"""Perform streaming post-alignment preparation -- de-duplication and sorting.
Centralizes a pipelined approach to generating sorted, de-duplicated BAM output
from sequencer results.
sambamba: https://github.com/lomereiter/sambamba
samblaster: http://arxiv.org/pdf/1403.7486v1.pdf
biobambam bammarkduplicates: http://a... | hjanime/bcbio-nextgen | bcbio/ngsalign/postalign.py | Python | mit | 7,133 | [
"BWA"
] | 59249e350e2d98ddba78911592876c7598c09fab3c1aadbff2da47dd3eb47b9f |
#
# ast_builder_test.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 License, or
# (at your option)... | kperun/nestml | tests/ast_builder_test.py | Python | gpl-2.0 | 2,997 | [
"VisIt"
] | 8036c4692b399dd5ee9b26cfa511f6e8d9691a9400a0401d1dee4c77e071015a |
# coding: utf-8
from __future__ import division, unicode_literals, print_function
import math
import os
import subprocess
import tempfile
import numpy as np
from monty.dev import requires
from monty.json import jsanitize
from monty.os import cd
from monty.os.path import which
from scipy.constants import e, m_e
from ... | aykol/pymatgen | pymatgen/electronic_structure/boltztrap.py | Python | mit | 92,713 | [
"ASE",
"BoltzTrap",
"VASP",
"pymatgen"
] | 53ab5e002d57f61cd5f8fd2a24107ef2248aaca5a801f1a3ecc68b6a2b55e24b |
import subprocess
import ssbio.utils
import os
import os.path as op
from collections import OrderedDict
def run_freesasa(infile, outfile, include_hetatms=True, outdir=None, force_rerun=False):
"""Run freesasa on a PDB file, output using the NACCESS RSA format.
Args:
infile (str): Path to PDB file... | SBRG/ssbio | ssbio/protein/structure/properties/freesasa.py | Python | mit | 4,076 | [
"Biopython"
] | 8c6ae81d8821227b6b02b7eb2ffb109d0b31c9547fcd0609a01bc988e3a13696 |
## Author: Aziz Khan
## License: GPL v3
## Copyright 2017 Aziz Khan <azez.khan__AT__gmail.com>
from django.shortcuts import render, get_object_or_404, redirect
from django.http import HttpResponse, HttpResponseRedirect
from django.http import JsonResponse
from django.core.paginator import Paginator, EmptyPage, PageNot... | asntech/jaspar | portal/views.py | Python | bsd-3-clause | 52,326 | [
"Biopython"
] | b69ce33171147b4feb307af9c85c682a84c093c5b4c5bae8cb18191941cada94 |
import csv
import datetime
import json
import mock
import os
import re
import shutil
import tempfile
import urllib
import pyquery
from cStringIO import StringIO
from nose.tools import eq_, ok_, assert_raises
from nose.plugins.skip import SkipTest
from django.test.client import RequestFactory
from django.test.utils im... | bsmedberg/socorro | webapp-django/crashstats/crashstats/tests/test_views.py | Python | mpl-2.0 | 194,868 | [
"VisIt"
] | 9552dccfefd014d6ca210950a32969fcaa679687b3a0cf7ea8dbffeca6737684 |
#!/usr/bin/python
"""Test to verify bug #353268 is still fixed.
Orca is double reading lines in openoffice with latest Ubuntu live CD.
"""
from macaroon.playback import *
import utils
sequence = MacroSequence()
######################################################################
# 1. Start oowriter.
#
sequence... | h4ck3rm1k3/orca-sonar | test/keystrokes/oowriter/bug_353268.py | Python | lgpl-2.1 | 4,251 | [
"ORCA"
] | 13dcadbd06173ecdf8a4b450689af476d1aa7788ebc28e2809ad130643d22670 |
import os
import re
import sys
import urllib
import BeautifulSoup
import json
#import simplejson
from models import Song as AppSong
import random
from django.http import HttpResponse
import logging
from django.core import serializers
URLS_LIST = ['http://pigeonsandplanes.com/', 'http://www.2dopeboyz.com/', 'http://agr... | zackster/HipHopGoblin | hhg/hhg_app/scraper.py | Python | bsd-3-clause | 3,878 | [
"VisIt"
] | 61f16c0127435a2932a8a21519b4c6256e6fc04262f0eef93c7aeae188fb41a0 |
import itertools
import sys
from ...utils.helpers import PickleSerializer
from ...exceptions import SmtlibError
from .expression import (
BitVecVariable,
BoolVariable,
ArrayVariable,
Array,
Bool,
BitVec,
BoolConstant,
ArrayProxy,
BoolEqual,
Variable,
Constant,
)
from .visito... | montyly/manticore | manticore/core/smtlib/constraints.py | Python | apache-2.0 | 16,759 | [
"VisIt"
] | d5b179fae42182df77ef12ecca77e4c5dcd166d6ad4c394849c47fc13ef79f86 |
'''
Code specific to Neuron devices
------------------------------------------
'''
import struct
import datetime
from dali.bus import Bus
import dali.gear.general
from math import sqrt
from tornado import gen
from tornado.ioloop import IOLoop
from modbusclient_tornado import ModbusClientProtocol, StartClient
from pym... | UniPiTechnology/evok | evok/neuron.py | Python | apache-2.0 | 116,035 | [
"NEURON"
] | e521a873dd7a9381be96d7dea249634691ffdcbb9412ec5dff4fe796284b7933 |
#!/usr/bin/env python
#
# Copyright 2013 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.
"""Convert Android xml resources to API 14 compatible.
There are two reasons that we cannot just use API 17 attributes,
so we are ge... | boundarydevices/android_external_chromium_org | build/android/gyp/generate_v14_compatible_resources.py | Python | bsd-3-clause | 13,731 | [
"Galaxy"
] | 36ca33f23698d0471ddfb407b62ba796e52315ff84f7b307dc0291bd0f4f188c |
"""
Interactivity functions and classes using matplotlib and IPython widgets
**Gravity forward modeling**
* :class:`~fatiando.gravmag.interactive.Moulder`: a matplitlib GUI for 2D
forward modeling using polygons
----
"""
from __future__ import division
import cPickle as pickle
import numpy
from matplotlib impor... | eusoubrasileiro/fatiando_seismic | fatiando/gravmag/interactive.py | Python | bsd-3-clause | 23,916 | [
"Gaussian"
] | 80365596eacbf6969839a35c0d457eaee137462c0b2fc34315e2fce3cf9f6b8f |
# coding=utf-8
# Copyright 2018 The Tensor2Tensor 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... | rsepassi/tensor2tensor | tensor2tensor/models/research/aligned.py | Python | apache-2.0 | 17,850 | [
"MOE"
] | 73aa8c5ccdef802b513942d12fd02911b0bd2b27e3fdb0a8fc4f64ae46c9d5c7 |
# ==================================================================================================
# Copyright 2011 Twitter, Inc.
# --------------------------------------------------------------------------------------------------
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... | foursquare/commons-old | src/python/twitter/pants/python/binary_builder.py | Python | apache-2.0 | 2,509 | [
"Brian"
] | 1775a4e98ad1385624c8187176e175b332cc9d08516e6b560f687e8fd4b488c0 |
import os, shutil, math
from datetime import datetime
from splinter import Browser
from itertools import combinations
from webmon.utils import _clean_filename, _rmsdiff
URLS = [
'http://www.mc706.com',
'http://www.google.com',
'http://www.reddit.com',
'http://www.msn.com',
]
PHOTOS_DIR = 'screenshots... | mc706/webmon | webmon/main.py | Python | mit | 2,220 | [
"VisIt"
] | 1c7be3eefba9616c1f70fcd4bcb043735e11e7ad76a44a49a4a0eb3bcc4f753e |
# Copyright (C) 2009 by Eric Talevich (eric.talevich@gmail.com)
# 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.
"""PhyloXML reader/parser, writer, and associated functions.
Instantiates tree elements... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/Phylo/PhyloXMLIO.py | Python | gpl-2.0 | 33,288 | [
"Biopython"
] | 9c166518cd6fe2ebff150589547a5deead5f6445d57065b5006b17029bbd0d0d |
#-*- coding: utf-8 -*-
# module pyparsing.py
#
# Copyright (c) 2003-2019 Paul T. McGuire
#
# 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... | xyuanmu/XX-Net | python3.8.2/Lib/site-packages/pip/_vendor/pyparsing.py | Python | bsd-2-clause | 245,385 | [
"VisIt"
] | b311947bf61c5810796681de7349b5889b60723e222affd219f740ff35426082 |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/gto/test/test_basis_parser.py | Python | apache-2.0 | 18,908 | [
"PySCF"
] | 9188fcd158ba060a957ef02dc418946c98815ee183c4445582e340740f62ad2f |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import vtk
def get_program_parameters():
import argparse
description = 'How to align two vtkPolyData\'s.'
epilogue = '''
'''
parser = argparse.ArgumentParser(description=description, epilog=epilogue,
formatter_cla... | lorensen/VTKExamples | src/Python/PolyData/AlignTwoPolyDatas.py | Python | apache-2.0 | 10,175 | [
"VTK"
] | 00ede6ac0b8ab97e359f66081e3b36939e2a4a7f692891402aaf3905e940dc6e |
#!/usr/bin/python
# -*- coding: utf-8 -*-
##################################################################################################
# module for the symmetric eigenvalue problem
# Copyright 2013 Timo Hartmann (thartmann15 at gmail.com)
#
# todo:
# - implement balancing
#
###########################... | kantel/processingpy | mpmathtest/mpmath/matrices/eigen_symmetric.py | Python | mit | 58,524 | [
"Gaussian"
] | d4f2ec6844b565f078572ccd35cbfba5bf7a28433e6d428e94dd535ee5d41a7f |
#
# Parse tree nodes for expressions
#
from __future__ import absolute_import
import cython
cython.declare(error=object, warning=object, warn_once=object, InternalError=object,
CompileError=object, UtilityCode=object, TempitaUtilityCode=object,
StringEncoding=object, operator=object,
... | thedrow/cython | Cython/Compiler/ExprNodes.py | Python | apache-2.0 | 450,199 | [
"VisIt"
] | 86bccd47993f69203123397f0033b6e5b66f26cfb57179240c6538efe4e864de |
"""
This module contains code for controlling the articulatory synthesizer at a high level.
"""
import audiosegment as asg
import collections
import copy
import experiment.configuration as configuration # pylint: disable=locally-disabled, import-error
import imageio
import itertools
import logging
import numpy as np
im... | MaxStrange/ArtieInfant | Artie/internals/motorcortex/motorcortex.py | Python | mit | 37,918 | [
"Gaussian"
] | 1958d1628bbe60d4688280e8dc7963d9f40b13377dc73531323ea22c88e80a6e |
#!/usr/bin/env python
"""
Serial version setup file
"""
print('building serial version')
## first load variables from PyMFEM_ROOT/setup_local.py
import sys
import os
ddd = os.path.dirname(os.path.abspath(os.path.realpath(__file__)))
root = os.path.abspath(os.path.join(ddd, '..', '..'))
sys.path.insert(0, root)
fro... | mfem/PyMFEM | mfem/_ser/setup.py | Python | bsd-3-clause | 4,193 | [
"VTK"
] | dd98c42d0b1e690ead702b2cd9100918587ebc30fd66f369568e12fb51970c53 |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2013, 2014, 2015 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 (at your optio... | SamiHiltunen/invenio-ext | invenio_ext/script/__init__.py | Python | gpl-2.0 | 12,586 | [
"VisIt"
] | 05885c7d27cbc9444a5b265e4d416c3b7964f9ff4cb562ec5dc53a7041e72a8d |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Regcm(AutotoolsPackage):
"""RegCM, ICTP Regional Climate Model (https://ictp.it)."""
... | LLNL/spack | var/spack/repos/builtin/packages/regcm/package.py | Python | lgpl-2.1 | 5,626 | [
"NetCDF"
] | 14671a08280fdc00eb2aef9ead352e499d1b9f164243f819ca63fa44f40f0c31 |
# Copyright 2010-2011 by Peter Cock. All rights reserved.
# 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.
"""Provides code to access the TogoWS integrated websevices of DBCLS, Japan.
This module ai... | bryback/quickseq | genescript/Bio/TogoWS/__init__.py | Python | mit | 13,050 | [
"BLAST",
"Biopython"
] | 4dfda1d05be2392993b07c463f0abbbc643211c80f4698e7fa59a8e1b16db0c0 |
from requests.auth import HTTPBasicAuth
from bs4 import BeautifulSoup
from . import nltk_utils
from time import time
import threading
import requests
import urllib2
import urllib
import json
bing_api = 'https://api.datamarket.azure.com/Bing/SearchWeb/v1/Web?$format=json&Query='
bing_key = 'IgVbvvtgQVYI7Yfu9hPgVx0Tmbih... | xirdneh/liveqa-trec-2016 | liveqa/websearch.py | Python | mit | 2,430 | [
"Galaxy"
] | 6fe1d7d2cea72157a317bdcea8fed0c8d721a73d02d6f46c6379ff491e2c43d8 |
## Copyright (C) 2011 Stellenbosch University
##
## This file is part of SUCEM.
##
## SUCEM is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Foundation, either version 3 of the License, or
## (at your option) any later v... | cemagg/sucem-fem | sandbox/pec_labels/dolfin_utils_meshconvert.py | Python | gpl-3.0 | 47,536 | [
"NetCDF"
] | 4b1190e45c863da4800c1c391c8b81b0704f85972d59f963237db5b2747e81c4 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
import django.contrib.gis.db.models.fields
import django.db.models.deletion
from django.conf import settings
import flooding_lib.models
import django_extensions.db.fields
import django_extensions.db.fields.json
c... | lizardsystem/flooding-lib | flooding_lib/migrations/0001_initial.py | Python | gpl-3.0 | 47,131 | [
"NetCDF"
] | f1f19aaa2a12d572954506f35b708566a57732c2016bc4309190ef802e167dd3 |
"""Integration with Python standard library module urllib2: Request class.
Copyright 2004-2006 John J Lee <jjl@pobox.com>
This code is free software; you can redistribute it and/or modify it
under the terms of the BSD or ZPL 2.1 licenses (see the file
COPYING.txt included with the distribution).
"""
import urllib2,... | jasrusable/fun | venv/lib/python2.7/site-packages/twill/other_packages/_mechanize_dist/_request.py | Python | gpl-2.0 | 3,236 | [
"VisIt"
] | b822e1f68154a7dcfda41baf75f1d04d3fd3c4900aef88e9405428faf87e9c85 |
# This is the code for experiments performed on the CIFAR-10 dataset for the DeLiGAN model. Minor adjustments
# in the code as suggested in the comments can be done to test GAN. Corresponding details about these experiments
# can be found in section 5.4 of the paper and the results showing the outputs can be seen in... | val-iisc/deligan | src/cifar/dg_cifar.py | Python | mit | 12,180 | [
"MOE"
] | b3b17c6fa9fdb25e7cdd26d1324cfbe34344cce51846626113bbc8b479321b31 |
# -*- coding: utf-8 -*-
"""
Created on Sun May 17 17:55:17 2015
Methods useful in bioinformatic algorithms
@author: Pablo the awesome molecular jedi
"""
# Libraries
from __future__ import division; # Needed in order to avoid weird rounding practices in Python 2
from builtins import str
from builtins import range
from ... | pablocarderam/genetargeter | py/utils/BioUtils.py | Python | mit | 17,935 | [
"Biopython"
] | 0a7638c36e1279b3243fc42915a5b9d19fb3384e56d911f814912ea5cc94860a |
# $Id$
#
# Copyright (C) 2007,2008 Greg Landrum
#
# @@ All Rights Reserved @@
#
import os,sys
import unittest
from rdkit.six.moves import cPickle
from rdkit import RDConfig
from rdkit import DataStructs as ds
def feq(v1,v2,tol=1e-4):
return abs(v1-v2)<tol
class TestCase(unittest.TestCase):
def setUp(self) :
p... | AlexanderSavelyev/rdkit | Code/DataStructs/Wrap/testSparseIntVect.py | Python | bsd-3-clause | 4,724 | [
"RDKit"
] | c25d605fee351683fcb3b06d2ea4fa11058f2701089c25cffb12fc935ffa16c0 |
#!/usr/bin/python
from nxs_utils import ThreadPool, Timer
import argparse, json, urllib2, multiprocessing, time, threading, thread, sys, datetime
from pprint import pprint
default_threads = multiprocessing.cpu_count()/2
# Blast given sequences (from json file) via neXtProt API sequencially + in parallel then check c... | calipho-sib/nextprot-scripts | src/nxs-test-blast-api.py | Python | gpl-2.0 | 5,666 | [
"BLAST"
] | 181585948eeee73a3c631036f9bd0ffe9892bb1ca6cac5dcf947464bb9d5e46e |
from __future__ import absolute_import
from .arc import ArcTrajectoryFile
from .dcd import DCDTrajectoryFile
from .binpos import BINPOSTrajectoryFile
from .xtc import XTCTrajectoryFile
from .trr import TRRTrajectoryFile
from .hdf5 import HDF5TrajectoryFile
from .netcdf import NetCDFTrajectoryFile
from .pdb import PDBT... | leeping/mdtraj | mdtraj/formats/__init__.py | Python | lgpl-2.1 | 659 | [
"NetCDF"
] | d845970c79306e8938e24c71bd100b524c4913af00fcb9673d99041d5d2a357c |
""" Python test discovery, setup and run of test functions. """
import fnmatch
import functools
import py
import inspect
import sys
import pytest
from _pytest.mark import MarkDecorator, MarkerError
from py._code.code import TerminalRepr
import _pytest
import pluggy
cutdir2 = py.path.local(_pytest.__file__).dirpath()
... | hunse/pytest | _pytest/python.py | Python | mit | 81,948 | [
"VisIt"
] | 557a57c56c45fb7e472503e646254caea46f9119b4ffb3a3cdfe76b161836bfe |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2013, 2014, 2015 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 (at your optio... | hachreak/invenio-ext | invenio_ext/script/__init__.py | Python | gpl-2.0 | 12,591 | [
"VisIt"
] | 0ec0b535685e3cf1f9f696fb166f7e13d98668f0be9415180c0892bb2e014a44 |
"""
=====
utils
=====
"""
def get_atomic_number_symbol(Z=None, symbol=None):
"""This function returns a tuple of matching arrays of atomic numbers
(Z) and chemical symbols (symbol).
:param Z: atomic numbers
:type Z: int, array like object of int's
:param symbol: chemical symbols
:type symbol:... | rosswhitfield/javelin | javelin/utils.py | Python | mit | 4,012 | [
"ASE"
] | 123c54f09c1beefdbb676860c2ff543f3b187d08c92740fbad007486cfc90ab0 |
########################################################################
# $HeadURL$
# File : HttpStorageAccessHandler.py
# Author : A.T.
########################################################################
""" The HttpStorageAccessHandler is a http server request handler to provide a secure http
access ... | rajanandakumar/DIRAC | DataManagementSystem/private/HttpStorageAccessHandler.py | Python | gpl-3.0 | 2,383 | [
"DIRAC"
] | 526550e57f3cd65f7f2e4a6196e7ce182da1ee67035f8d56d57b719407ea182c |
'''
Spike-timing dependent plasticity
Adapted from Song, Miller and Abbott (2000) and Song and Abbott (2001)
'''
###############################################################################
## PARAMETERS
# select code generation standalone device
devicename = 'cuda_standalone'
# devicename = 'cpp_standalone'
# nu... | brian-team/brian2cuda | examples/stdp.py | Python | gpl-2.0 | 6,236 | [
"NEURON"
] | 7664fc8c438160fab2a6c2738f24fa91e6596d66553e93e17c26de4cbee46ee4 |
"""
.. moduleauthor:: Johan Comparat <johan.comparat__at__gmail.com>
General purpose:
................
The class StellarMassFunction is a wrapper dedicated to handling the fit of stellar mass function.
*Imports*::
import numpy as np
import astropy.io.fits as pyfits
import astropy.units as u
import glob
import... | JohanComparat/pySU | spm/python/StellarMassFunction.py | Python | cc0-1.0 | 4,619 | [
"Galaxy"
] | 3d4eac3eccd3ab6773c0662adf825951fce455157686ab96f1d2b1eeccfd680f |
import click
from parsec.cli import pass_context, json_loads
from parsec.decorators import custom_exception, json_output
@click.command('show_dataset_provenance')
@click.argument("history_id", type=str)
@click.argument("dataset_id", type=str)
@click.option(
"--follow",
help="If ``True``, recursively fetch dat... | galaxy-iuc/parsec | parsec/commands/histories/show_dataset_provenance.py | Python | apache-2.0 | 2,190 | [
"Galaxy"
] | 2ca96e455046bdf05f8de2e75ce62eaf4554b93093af28ff6bbbc80f88133597 |
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