text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
# -*- coding: utf-8 -*-
#
# This file is part of Invenio-Query-Parser.
# Copyright (C) 2014 CERN.
#
# Invenio-Query-Parser 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 ... | jalavik/invenio-query-parser | invenio_query_parser/ast.py | Python | gpl-2.0 | 4,005 | [
"VisIt"
] | cb1f07f54c59af16b031ad401ad65b81b0ca7c68235ac0d023bd7585fc39ebce |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/e2openplugin-OpenWebif | plugin/controllers/views/web/remotecontrol.py | Python | gpl-2.0 | 5,217 | [
"VisIt"
] | 2477d05673dc1b4fd8f50b864316f34be97e3a82386c7b2dd6b2701c3249f271 |
"""Mayavi/traits GUI for averaging two sets of KIT marker points."""
# Authors: Christian Brodbeck <christianbrodbeck@nyu.edu>
#
# License: BSD (3-clause)
import os
import sys
import numpy as np
from mayavi.tools.mlab_scene_model import MlabSceneModel
from pyface.api import confirm, error, FileDialog, OK, YES
from ... | adykstra/mne-python | mne/gui/_marker_gui.py | Python | bsd-3-clause | 15,393 | [
"Mayavi"
] | e086238c5e03a0123e0934c3b212f4791ba8a35e498d6801a27704f115da9164 |
import pytest
from qcelemental.util import which_import, parse_version
def is_psi4_new_enough(version_feature_introduced):
if which_import('psi4') is None:
return False
import psi4
return parse_version(psi4.__version__) >= parse_version(version_feature_introduced)
using_psi4 = pytest.mark.skipi... | loriab/pylibefp | tests/addons.py | Python | bsd-3-clause | 655 | [
"Psi4"
] | 2dc7a4e42061ca853e7543e025b90a255953b7d97518a453c36543909606cdc9 |
# Function to find the MCS from a mol object queue
from com.im.lac.types import MoleculeObjectIterable
from java import lang
import sys
from java.util import ArrayList
from java.lang import Thread, InterruptedException
from java.lang import Class
lang.System.loadLibrary('GraphMolWrap')
# Pull it in as a stream of stri... | InformaticsMatters/squonk | components/rdkit-camel/src/main/python/find_mcs.py | Python | apache-2.0 | 1,073 | [
"RDKit"
] | cfedbb2ef2f63b2fcfb684d69064964f42883c0329d077b15b8c21142fae04c5 |
import galaxy.model
from galaxy.model.orm import *
from galaxy.model.mapping import context as sa_session
from base.twilltestcase import TwillTestCase
""" A sample analysis"""
class AnalysisDNAseHSSFlankedGenes( TwillTestCase ):
def test_get_DNAseHSS_flanked_genes( self ):
self.logout()
self.login... | volpino/Yeps-EURAC | test/functional/test_DNAse_flanked_genes.py | Python | mit | 4,661 | [
"Galaxy"
] | dfabe31545fb37fbe42b4af42bee366b8f27f3b9385a1c6790b0aad089edf091 |
# proxy module
from __future__ import absolute_import
from mayavi.modules.streamline import *
| enthought/etsproxy | enthought/mayavi/modules/streamline.py | Python | bsd-3-clause | 94 | [
"Mayavi"
] | f47bec3f3b0602e9d7d6447bcbefbcb755af9966e7de83a8c16477ffeb900982 |
__source__ = 'https://leetcode.com/problems/island-perimeter/'
# Time: O(n)
# Space: O(1)
#
# Description: Leetcode # 463. Island Perimeter
# Though: what if theres' a lake?
# Lake: [[0,1,0,0],[1,0,1,0],[0,1,0,0],[1,1,0,0]]
# No Lake: [[0,1,0,0],[1,1,1,0],[0,1,0,0],[1,1,0,0]]
# -> both works
# You are given a map i... | JulyKikuAkita/PythonPrac | cs15211/IslandPerimeter.py | Python | apache-2.0 | 5,998 | [
"VisIt"
] | dfa9f402bd498c7f07914225ce46a966452c957115f8cc0383e730b169271a84 |
import sys
def has_colors(stream):
"""
Determine if the terminal supports ansi colors.
"""
if not hasattr(stream, "isatty"):
return False
if not stream.isatty():
return False # auto color only on TTYs
try:
import curses
curses.setupterm()
return curses.... | nickjj/ansigenome | ansigenome/color.py | Python | gpl-3.0 | 1,571 | [
"Brian"
] | a95dbf26823028df8fa6928cadbeaeef39b6e1b6332ee3a09fae0d473642831d |
import logging
from DOM import Window, DFT
from DOM.W3C import w3c
from DOM import MIMEHandler, SchemeHandler
from ThugAPI.ThugOpts import ThugOpts
from ThugAPI.ThugVulnModules import ThugVulnModules
consolehandler = logging.StreamHandler()
logging.getLogger().addHandler(consolehandler)
logging.getLogger().setLevel... | max0d41/ThugBrowser | src/test.py | Python | gpl-2.0 | 1,871 | [
"ADF"
] | 87843feb2b146f5f0a7bdd704061256ef0b0682cc46b15c7d4d49640380ec8e7 |
# Copyright (C) 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 versio... | espressomd/espresso | testsuite/scripts/tutorials/test_langevin_dynamics.py | Python | gpl-3.0 | 1,345 | [
"ESPResSo"
] | 10ae558b59059d3fd1784d018023feb21bed86f14c5b4c8a7b7626442a5be5ed |
import datetime
import re
import secrets
import time
from datetime import timedelta
from typing import (
AbstractSet,
Any,
Callable,
Dict,
List,
Optional,
Pattern,
Sequence,
Set,
Tuple,
TypeVar,
Union,
)
import django.contrib.auth
import orjson
import re2
from bitfield i... | andersk/zulip | zerver/models.py | Python | apache-2.0 | 168,463 | [
"VisIt"
] | 7aeac86de6c5f60043a78b518e2aee2a519031f0c8f37b8c061e22203d6165d8 |
from mpi4py import MPI
from lammps import PyLammps
L = PyLammps()
L.file('in.melt')
if MPI.COMM_WORLD.rank == 0:
pe = L.eval("pe")
print("Potential Energy:", pe)
| stanmoore1/lammps | python/examples/pylammps/mpi4py/melt.py | Python | gpl-2.0 | 173 | [
"LAMMPS"
] | 004846f50a219e4e354fa14ae273b1a72ec2b28f0e4078cd05eaa21d62180ec5 |
# Orca
#
# Copyright 2004-2009 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | GNOME/orca | src/orca/settings.py | Python | lgpl-2.1 | 13,188 | [
"ORCA"
] | 063fbb3ee65c9a5a281411667696087021a660bc23c75493aa222ccd78f169e2 |
#
# Copyright (C) 2009, 2015, 2016, 2019, 2020, 2021
# Smithsonian Astrophysical Observatory
#
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at y... | anetasie/sherpa | sherpa/astro/flux.py | Python | gpl-3.0 | 26,622 | [
"Gaussian"
] | ea01c6aa75f87add41c1f10afb99c779e44af41b5542e6088d75c6933502d9b6 |
import os
import sys
import unittest
import pytest
from nbodykit.extern.six.moves.urllib import request
from nbodykit import examples_dir
def user_cache_dir(appname):
r"""
This function is copied from:
https://github.com/pypa/pip/blob/master/pip/utils/appdirs.py
Return full path to the user-specific... | rainwoodman/nbodykit | nbodykit/test/__init__.py | Python | gpl-3.0 | 4,568 | [
"NetCDF"
] | 0d18d8538d9da41a010ddf50faf8574e74a5a5bdac5bd3000ca8622d35d8b2a8 |
import unittest
import tempfile
import os
import numpy as np
import six
from collections import OrderedDict
import caffe
def simple_net_file(num_output):
"""Make a simple net prototxt, based on test_net.cpp, returning the name
of the (temporary) file."""
f = tempfile.NamedTemporaryFile(mode='w+', delete... | CivilNet/Gemfield | dockerfiles/py-faster-rcnn/files/gemfield/py-faster-rcnn/caffe-fast-rcnn/python/caffe/test/test_net.py | Python | gpl-3.0 | 11,636 | [
"Gaussian"
] | 1550253bc35ec53e87f461ce8c1e950dd87eb36c6770c15e5eae1d31d3cce64b |
# -*- coding: utf-8 -*-
#
# This file is part of Invenio.
# Copyright (C) 2013 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 option) any later... | CERNDocumentServer/invenio | modules/bibcheck/lib/plugins/dates.py | Python | gpl-2.0 | 2,836 | [
"VisIt"
] | 1e7e5ee5663674b17f2f3d9b36595cda6a4e961d90e54b7fb8c23cee0f512831 |
#!/usr/bin/env python
# $Id: overlayExample.py 545 2012-01-18 06:10:03Z cvermilion $
#----------------------------------------------------------------------
# Copyright (c) 2010-12, Pierre-Antoine Delsart, Kurtis Geerlings, Joey Huston,
# Brian Martin, and Christopher Vermilion
#
#----------------------... | mickypaganini/SSI2016-jet-clustering | spartyjet-4.0.2_mac/examples_py/overlayExample.py | Python | mit | 3,193 | [
"Brian"
] | 4ccf7a61dbacf3c592a99d24dcf058f55da0f5362e3eb6bc05a387ad2b5d327a |
from __future__ import print_function
from discomark.models import *
from discomark import utils
import datetime
import io
import os
import re
import shutil
import subprocess
import sys
from glob import glob
from Bio import SeqIO, AlignIO
from Bio.Align import AlignInfo
from Bio.Align import MultipleSeqAlignment
#from ... | hdetering/discomark | discomark/steps.py | Python | gpl-2.0 | 15,525 | [
"BLAST"
] | ee2ce5af75bf0097be733a228ea5413ef7708a0117294bbb88734ec4a7d5053f |
from octopus.runtime import *
from octopus.sequence.control import Bind
from twisted.internet import defer
defer.Deferred.debug = True
v = variable(0, "i", "i")
d = variable(False, "b", "b")
d_ctrl = Bind(d, v, lambda x: x > 5)
s = sequence(
log("Running"),
loop_while(v < 10, [
increment(v),
log("v = " + v + ... | rasata/octopus | examples/test_bind.py | Python | mit | 416 | [
"Octopus"
] | 57c9b333100e69d18e0e3dd992ac76fc28724ff91864209600ebcc0ef0a38175 |
import sympy
from sympy.functions import DiracDelta, Heaviside
from sympy.simplify.simplify import simplify
from sympy.solvers import solve
from sympy.utilities.misc import default_sort_key
def change_mul(node, x):
"""change_mul(node, x)
Rearranges the operands of a product, bringing to front any simple
... | Cuuuurzel/KiPyCalc | sympy_old/integrals/deltafunctions.py | Python | mit | 5,124 | [
"DIRAC"
] | 216e6cbfd2672505a398cb6321cfb8d4e7d2d6a2ca7a5ca435ab8dd0d37c4543 |
#!/usr/bin/env python
# *- coding: utf-8 -*-
# vim: set expandtab tabstop=4 shiftwidth=4 softtabstop=4 textwidth=79:
import math
from drdisco import log
from drdisco.DetectFrameShifts import DetectFrameShifts
from drdisco.utils import reverse_complement, is_gzip
import gzip
import HTSeq
from tqdm import tqdm
from pyf... | yhoogstrate/dr-disco | drdisco/DetectOutput.py | Python | gpl-3.0 | 37,249 | [
"HTSeq"
] | 8d4316c995d54efdd8c9271ae654fa78f9540dfeb8566f986c5313166ea29c84 |
# coding=utf-8
from datetime import timedelta
from django.contrib.auth.tokens import default_token_generator
from django.core import mail
from django.core.urlresolvers import reverse
from django.test import LiveServerTestCase
from django.utils.timezone import now
from django.utils.http import urlsafe_base64_encode
from... | brianwc/courtlistener | cl/users/tests.py | Python | agpl-3.0 | 6,020 | [
"VisIt"
] | dd87cd3e4c1019c2f61d7fbe2dbde13c6a2009355938cbfe3d3ab63847667f74 |
# Physical quantities with units
#
# Written by Konrad Hinsen <hinsen@cnrs-orleans.fr>
# with contributions from Greg Ward
# last revision: 2007-5-25
#
# This file come from the ScientificPython library and is written by Konrad Hinsen
# https://bitbucket.org/khinsen/scientificpython
"""
Physical quantities with unit... | mupif/mupif | obsolete/physics/physicalquantities.py | Python | lgpl-3.0 | 34,922 | [
"Avogadro"
] | 75bae913388e365549713941ea62c70572f90a48b7f2744e4bd3f5755689ca7d |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | TheTimmy/spack | var/spack/repos/builtin/packages/r-ape/package.py | Python | lgpl-2.1 | 2,564 | [
"Bioconductor"
] | ab278f7bd03a39d3782e17e97fc6a2f037400995d7105de609c64f79c5fc1d1d |
import sip
sip.setapi('QString', 1)
import sys
import math
import os
import ctypes
from time import sleep
from PyQt4 import QtCore, QtNetwork
from numpy import *
from pykstpp import *
def b2str(val):
if isinstance(val, bool):
return "true" if val else "false"
else:
return str(val)
class Client:
""" Thi... | RossWilliamson/kst_old | pyKst/pykst.py | Python | gpl-2.0 | 109,255 | [
"Gaussian"
] | 18272c818c1ce6bdabcead73f1bf175d1a59e1e8d6530b8c5571ec1eb0bd63ae |
# Functions to implement several important functions for
# various Continous and Discrete Probability Distributions
#
# Author: Travis Oliphant 2002-2011 with contributions from
# SciPy Developers 2004-2011
#
import math
import warnings
from copy import copy
from scipy.misc import comb, derivative
from s... | ygenc/onlineLDA | onlineldavb_new/build/scipy/scipy/stats/distributions.py | Python | gpl-3.0 | 213,950 | [
"Gaussian"
] | bda2547267022774c4e3b54f5706a0ce3bc7365e8b23655578e0517d40920fe4 |
# -*- coding: utf-8 -*-
#
# test_spatial_kernels.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 Li... | hakonsbm/nest-simulator | topology/pynest/tests/test_spatial_kernels.py | Python | gpl-2.0 | 31,423 | [
"Gaussian",
"NEURON"
] | c8e17a34199b55c635bc6bea0bb99174fadc3f9b57a28cbaac76816d08d91d92 |
import wikipedia
import asyncio
import re
import wolframalpha
import discord
import string
import hashlib
from addons import utils
from datetime import datetime
from discord.ext import commands
from random import choice
class General:
"""
General Chat Commands
"""
# Construct
def __init__(self, b... | RIP95/kurisu-bot | addons/general.py | Python | mit | 14,399 | [
"VisIt"
] | 988a2e29119325b70ee21232d142ed1e3433a50cb438aedcdbb98738aecb0dcf |
# $Id$
#
# Copyright (C) 2003 Rational Discovery LLC
# All Rights Reserved
#
import sys
from rdkit import six
from rdkit.VLib.Node import VLibNode
class SupplyNode(VLibNode):
""" base class for nodes which supply things
Assumptions:
1) no parents
Usage Example:
>>> supplier = SupplyNode(conten... | adalke/rdkit | rdkit/VLib/Supply.py | Python | bsd-3-clause | 1,432 | [
"RDKit"
] | 6fc00c1db28dd7c56bca877f5d87c0b20cd6c5feab45127a012acb17a7e11aa0 |
import subprocess, os, re, math, time
from web_frontend import settings, condor_spec
from lxml import etree
from string import Template
xmlns = '{http://www.copasi.org/static/schema}'
condor_string_body = """transfer_input_files = ${copasiFile}${otherFiles}
log = ${copasiFile}.log
error = ${copasiFile}.err
output =... | Nucleoos/condor-copasi | web_frontend/copasi/model.py | Python | artistic-2.0 | 143,791 | [
"COPASI"
] | 4707b3a5c9d015d598b43301d98c85dc657f199759d3da7c9c618fcb4c58bdde |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | alejob/mdanalysis | package/MDAnalysis/topology/tables.py | Python | gpl-2.0 | 6,340 | [
"Amber",
"CHARMM",
"GROMOS",
"Gromacs",
"MDAnalysis"
] | 4ccf18b5e4e7108a4d49f3b3ba02e720cf89facdc12f86572e3bc69bd63b6fd5 |
# ============================================================================
#
# Copyright (C) 2007-2010 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | kurtraschke/camelot | camelot/core/utils.py | Python | gpl-2.0 | 7,357 | [
"VisIt"
] | 4e8c78354016f54bd0f08fe9216de0f0ea2561fb36e71e446e1e16371e1d353a |
# -*- coding: utf-8 -*-
# Copyright 2007-2016 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at... | to266/hyperspy | hyperspy/models/model1D.py | Python | gpl-3.0 | 32,769 | [
"Gaussian"
] | e1ce400442935fcde65325a21a6c49587ab883c67cd4aba7f15a685e889c815e |
"""
Class that holds a fit page state
"""
# TODO: Refactor code so we don't need to use getattr/setattr
################################################################################
# This software was developed by the University of Tennessee as part of the
# Distributed Data Analysis of Neutron Scattering Exper... | lewisodriscoll/sasview | src/sas/sasgui/perspectives/fitting/pagestate.py | Python | bsd-3-clause | 58,060 | [
"Gaussian"
] | d649546fe8d71e3478184ab71bc9e2bc4303eb9ef12f7153ec32433dfca54f3d |
from electrum.util import print_error
import httplib, urllib
import socket
import threading
import hashlib
import json
from urlparse import urlparse, parse_qs
try:
import PyQt4
except Exception:
sys.exit("Error: Could not import PyQt4 on Linux systems, you may try 'sudo apt-get install python-qt4'")
from PyQt... | mazaclub/electrum-nmc | plugins/labels.py | Python | gpl-3.0 | 9,132 | [
"VisIt"
] | d3a52f4b8a48130aa1777b0d900976dd77aa1c9f21fc60b052c40302f0a5e86d |
#!/usr/bin/python
## Global modules
import os
from os.path import join
import logging
import shutil
import pysam
## Local modules
import mglobals
import helpers
import combining_SNPs_with_vcf as combine_w_vcf
log = logging.getLogger('pipeline')
@helpers.log_func
def my_tophat():
if mglobals.original:
... | d-quinn/bio_quinn2013 | parental_alignment/pipeline-singleend_altfastas.py | Python | mit | 11,911 | [
"pysam"
] | c8976078e8fdc35df759a9f4934fe8a33850f69a93a4920703692798ba5e8483 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | tensorflow/tensorflow | tensorflow/python/ops/control_flow_grad.py | Python | apache-2.0 | 9,501 | [
"VisIt"
] | 83abb9b5df74446633207718ab61d4cae624eeed6d0cbeebb02dbb1d5822433e |
import pandas as pd
import re
import os.path
import itertools
from sys import argv
script, cluster_name, itineration = argv
table2_df = pd.read_csv('../tables/%s_table2_%s.csv'%(cluster_name,itineration), sep='\t')
col1 = []
col2 = []
col3 = []
col4 = []
col5 = []
col6 = []
col7 = []
col8 = []
col9 = []
for index, ... | tiagolbiotech/BioCompass | BioCompass/edges_gen.py | Python | bsd-3-clause | 2,526 | [
"BLAST"
] | 63a9654583db1c491da9741831dc3f1965a0461a6066deaa7d3423b92bb30033 |
"""transfer_function.py: Calculates transfer function of leaky
integrate-and-fire neuron fed by filtered noise [1,2].
[1] Schuecker et al., "Modulated escape from a metastable state driven
by colored noise", Phys. Rev. E (2015)
[2] Schuecker et al., "Reduction of colored noise in excitable systems
to white noise and d... | INM-6/neural_network_meanfield | transfer_function.py | Python | gpl-3.0 | 4,817 | [
"NEURON"
] | 028ed15a82dbcb8d546432954d1379a99ee55fe133fef626f46b55b1dea4cc7f |
"""
=============================
Ledoit-Wolf vs OAS estimation
=============================
The usual covariance maximum likelihood estimate can be regularized
using shrinkage. Ledoit and Wolf proposed a close formula to compute
the asymptotically optimal shrinkage parameter (minimizing a MSE
criterion), yielding th... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/examples/covariance/plot_lw_vs_oas.py | Python | mit | 2,950 | [
"Gaussian"
] | f00c7f34c73f1dc3ae1fdd0c02646a6f23df0963facb406e346ea90f35a360cb |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | lhfei/spark-in-action | spark-3.x/src/main/python/mllib/gaussian_mixture_model.py | Python | apache-2.0 | 2,694 | [
"Gaussian"
] | 07481b8ab47c796b869c47e121d924b71b41da492d67d912cbcb3c682c4d34d6 |
################################################################################
# JobBoard: a simple Django-based job board
# Copyright (c) 2009, Imaginary Landscape
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided... | ImaginaryLandscape/iscape-jobboard | jobboard/tests.py | Python | bsd-3-clause | 28,923 | [
"VisIt"
] | c5be7f64003fe3454d564f1ab7f451c9cc8d5dcaabfccbbc70d205e00334e89f |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2014 Stanford University and the Authors
#
# Authors: Jason Swails
# Contributors:
#
# This code for reading Amber r... | casawa/mdtraj | mdtraj/formats/amberrst.py | Python | lgpl-2.1 | 33,281 | [
"Amber",
"MDTraj",
"NetCDF"
] | 0abd5ae0406e572aa062f6ff73e1c4437caf84d6026304914f5de102b03199fa |
# This file is part of the Frescobaldi project, http://www.frescobaldi.org/
#
# Copyright (c) 2008 - 2014 by Wilbert Berendsen
#
# 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
... | shimpe/frescobaldi | frescobaldi_app/scorewiz/parts/plucked_strings.py | Python | gpl-2.0 | 13,709 | [
"ADF"
] | 7b5130e3ce9172832932b39c0b6229e817c88b5d6dc53efda30d7faafdb9daf6 |
# Miro - an RSS based video player application
# Copyright (C) 2005, 2006, 2007, 2008, 2009, 2010, 2011
# Participatory Culture Foundation
#
# 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; eithe... | rwaldron/mirovideoconverter3 | mvc/widgets/gtk/window.py | Python | gpl-3.0 | 25,690 | [
"VisIt"
] | e1e29cd9e1a108a9c36a545636a8ad634b86b21c12c91eebf4463ef36189c334 |
# -*- coding: utf-8 -*-
# Copyright 2020 Google LLC
#
# 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... | googleapis/python-api-core | tests/unit/operations_v1/test_operations_rest_client.py | Python | apache-2.0 | 35,740 | [
"Octopus"
] | a3cc8ee1e11170db7b439a2c4302394b423ce81b36d546d5165e35f2c0373e92 |
#!/usr/bin/env python
"""This is the training script for the model.
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import os
import sys
import cPickle as pickle
import time
import numpy as np
import tensorflow as tf
from model import helper
from mo... | hao-cheng/factored_neural | factored_neural/train_model.py | Python | apache-2.0 | 7,239 | [
"Gaussian"
] | d70735ea31233ec656943b4528ed7b87041467c14bef0a6d8fc84a984bfdc1e1 |
import truetypetracer as ttt # https://github.com/aewallin/truetype-tracer
import openvoronoi as ovd # https://github.com/aewallin/openvoronoi
import ovdvtk
import time
import vtk
def drawLoops(myscreen, loops, loopColor):
# draw the loops
nloop = 0
for lop in loops:
n = 0
N = len(lop)
... | aewallin/openvoronoi | python_examples/ttt/ttt_1.py | Python | lgpl-2.1 | 6,129 | [
"VTK"
] | 558a8ad74baa6f294f803b35a3671a0e0459b630a99f5f89ecf2c2c6bb34ed49 |
"""
Connected components.
"""
import logging
import itertools
import numpy as np
from matplotlib.patches import FancyArrowPatch, Circle
import networkx as nx
from networkx.algorithms.traversal import bfs_tree
from networkx.algorithms.components import is_connected
from monty.json import MSONable
from monty.json imp... | mbkumar/pymatgen | pymatgen/analysis/chemenv/connectivity/connected_components.py | Python | mit | 42,585 | [
"pymatgen"
] | 545e61b4ee282bc06b7cb528cfa19bcdcb45f503391f42bf7cf7129e77e8d91a |
import os
try:
from setuptools import setup
except ImportError:
from distutils.core import setup
DESCRIPTION = "Galaxy Cluster and Weak Lensing Tools"
LONG_DESCRIPTION = """
cluster-lensing: galaxy cluster halo calculations
======================================================
This package includes tools for ... | jesford/cluster-lensing | setup.py | Python | mit | 1,647 | [
"Galaxy",
"VisIt"
] | 9ed923b0693fc7d3504b9ff35d125a9e150d78e15e80a534a816e0b05c35427a |
#!/usr/bin/env python
"""Python script to run cell model"""
"""
/* Copyright (c) 2015 EPFL-BBP, All rights reserved.
THIS SOFTWARE IS PROVIDED BY THE BLUE BRAIN PROJECT ``AS IS''
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICU... | cigani/NEST | L5_TTPC1_cADpyr232_1/run.py | Python | mit | 6,278 | [
"NEURON",
"VisIt"
] | 5ea3fb18e8f30f2bfaa1b7b5357aa229daba2471557ba676f302dfdc7daf4244 |
"""
Page object for Bitcoin main Page.
"""
import os
import sys
sys.path.append(os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
import conf.locators_conf as locators
from utils.Wrapit import Wrapit
from .Mobile_Base_Page import Mobile_Base_Page
class Bitcoin_Main_Page(Mobile_Base_Page):
"Page object ... | qxf2/qxf2-page-object-model | page_objects/bitcoin_main_page.py | Python | mit | 2,234 | [
"VisIt"
] | 7802825e6e1e97a45c5e514e5eb6da23b0b111bab23ed7507fed6b613e2c1a02 |
# Copyright 2012 Jake Ross
#
# 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, soft... | USGSDenverPychron/pychron | pychron/mv/locator.py | Python | apache-2.0 | 29,612 | [
"Gaussian"
] | bffcf5ec871da1b18c77b9336a402bf973abcbbf99e6227c8c1de86173f0df0d |
# Copyright (C) 2011, 2012, 2013, 2015, 2016 David Maxwell and Constantine Khroulev
#
# This file is part of PISM.
#
# PISM 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 (... | talbrecht/pism_pik | site-packages/PISM/util.py | Python | gpl-3.0 | 3,498 | [
"NetCDF"
] | 8bc3fa8333bbc28d5888ae9c6134249f611a6d56d5b6bcfb0078d1f8a07f8908 |
###############################
# This file is part of PyLaDa.
#
# Copyright (C) 2013 National Renewable Energy Lab
#
# PyLaDa is a high throughput computational platform for Physics. It aims to make it easier to submit
# large numbers of jobs on supercomputers. It provides a python interface to physical input, suc... | pylada/pylada-light | src/pylada/ipython/manipfolders.py | Python | gpl-3.0 | 12,076 | [
"CRYSTAL",
"VASP"
] | d8c3e295d4cec699b4d696fac62412fb2b2fbd43f56e01c754e1f1f990340250 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
from math import sin, cos, asin, pi, degrees, radians
import os
import numpy as np
import json
from .core import DiffractionPattern, DiffractionPatternCalcul... | nisse3000/pymatgen | pymatgen/analysis/diffraction/neutron.py | Python | mit | 8,012 | [
"CRYSTAL",
"pymatgen"
] | 929a9162eb1bf133ad0e15688e08156844a984d04f9f0c3dca88a4acb7c59f91 |
import Bio.PDB as biopython
import os, subprocess, shutil
#########################################
def get_biopython_structure(params):
currdir = params.rundirs.in_dir
os.chdir("/".join([params.run_options.workdir, currdir]))
pdbname = params.run_options.pdb
parser = biopython.PDBParser(QUIET=True) # silenc... | ivanamihalek/smallmol | modeling_lib/pdb_doctor.py | Python | gpl-2.0 | 5,248 | [
"Biopython"
] | 63d3fecb9bde735a9b428fc5f39a2a9ec02d2fd27970d1057f81822e8e8957cf |
# coding=utf-8
import io
import os
import re
from setuptools import setup, find_packages
def get_path(*args):
return os.path.join(os.path.dirname(__file__), *args)
def read_from(*args):
filepath = get_path(*args)
with io.open(filepath, 'rt', encoding='utf8') as f:
return f.read()
data = read_f... | jpscaletti/rev-assets | setup.py | Python | bsd-3-clause | 1,487 | [
"GULP"
] | 71f24f1c5ea295bd2b007a985c312cfa0f0a720be2dff719181d3d64d043add9 |
# freeseer - vga/presentation capture software
#
# Copyright (C) 2014 Free and Open Source Software Learning Centre
# http://fosslc.org
#
# 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, ei... | Freeseer/freeseer | src/freeseer/plugins/output/raw_output/__init__.py | Python | gpl-3.0 | 3,452 | [
"VisIt"
] | 2a700bb885691284433fac9d94ac5af2877fb3519a0883d6a722b1336d23855b |
###BAMtoJunctionBED
#Author Nathan Salomonis - nsalomonis@gmail.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
#to use... | nsalomonis/AltAnalyze | import_scripts/BAMtoBarcode.py | Python | apache-2.0 | 11,193 | [
"pysam"
] | 1df7998017b8fafd5f996c9337cde9349ba19edbbfc108666b8c8c775b505c5b |
# ==================================================================================================
# Copyright 2011 Twitter, Inc.
# --------------------------------------------------------------------------------------------------
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... | imsut/commons | src/python/twitter/common/contextutil/__init__.py | Python | apache-2.0 | 5,714 | [
"Brian"
] | 827d887a340b3e7a6cd4aa212a62ef0c1cc165a9e370c34ca94294e0aefe9e09 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
from pathlib import Path
import numpy as np
from pymatgen.core.structure import Molecule, Structure
from pymatgen.io.cp2k.inputs import Coord, Cp2kInput, Keyword, KeywordList, Kind
from pymatgen.util.testing ... | materialsproject/pymatgen | pymatgen/io/cp2k/tests/test_inputs.py | Python | mit | 5,209 | [
"CP2K",
"pymatgen"
] | 2e3d0da7ced3774dd62927184d845d4c6b595f1c72699282054839b1858e59e6 |
# encoding:utf-8
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2009 Benny Malengier
#
# 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 of the License, or
# ... | beernarrd/gramps | gramps/plugins/textreport/textplugins.gpr.py | Python | gpl-2.0 | 14,633 | [
"Brian"
] | 8d3356a03491d2aeeca35522ea79533427741de8bf2718df68d11dc8f3947377 |
import polypasswordhasher
from unittest import TestCase
import sys
THRESHOLD = 10
class TestPolyPasswordHasher(TestCase):
def test_polypasswordhasher(self):
# require knowledge of 10 shares to decode others. Create a blank, new
# password file...
pph = polypasswordhasher.PolyPasswordHasher(threshol... | PolyPasswordHasher/PolyPasswordHasher | python-reference-implementation/test/testpolypasswordhasher.py | Python | mit | 5,324 | [
"MOE"
] | 5eadcbc2fd68a5969b83b1c0537a39b8e22979745fa7574b4b7f9a6a3b5cae95 |
#!/usr/bin/env python
#
# Copyright 2008,2009,2011,2012,2015 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# GNU Radio is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3, or... | awalls-cx18/gnuradio | gr-uhd/apps/uhd_siggen_base.py | Python | gpl-3.0 | 13,141 | [
"Gaussian"
] | 11ce478040c4414bc4071681d1b7a348021a499eee1cd6443dd843eb8ce7f2a0 |
# Copyright 2017 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | jazcollins/models | lfads/lfads.py | Python | apache-2.0 | 83,844 | [
"Gaussian"
] | 4d1f75546d6139c87c8d42077b229d42ab409da1bb1640f0f4947b49c9d1985a |
#!/usr/bin/env python
# Copyright 2014-2019 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... | gkc1000/pyscf | pyscf/shciscf/examples/01_O2_PT.py | Python | apache-2.0 | 2,512 | [
"PySCF"
] | ec6753f38fdd1d8abb7f299233f9ea64cbc86f545318c7c11f965d5ce2ce7ec7 |
# (c) Crown Owned Copyright, 2016. Dstl.
from django.contrib.auth import get_user_model
from django.core.urlresolvers import reverse
from django_webtest import WebTest
from apps.organisations.models import Organisation
from apps.teams.models import Team
class UserWebTest(WebTest):
def test_update_button_shows_... | dstl/lighthouse | apps/accounts/tests/test_user_update.py | Python | mit | 10,152 | [
"VisIt"
] | 91d0a07a95bf51cb44c41777f66f666150be786ab683355da8e6c8f7a6c7bcf3 |
from __future__ import absolute_import
from typing import Any, DefaultDict, Dict, List, Set, Tuple, TypeVar, Text, \
Union, Optional, Sequence, AbstractSet, Pattern, AnyStr, Callable, Iterable
from typing.re import Match
from zerver.lib.str_utils import NonBinaryStr
from django.db import models
from django.db.mode... | vaidap/zulip | zerver/models.py | Python | apache-2.0 | 78,060 | [
"VisIt"
] | 919ea79dc486bdf4ff661245b87213bba0f146ca2fb863945a1fe7732c436047 |
""" This module exposes the BaseClient class,
which serves as base for InnerRPCClient and TransferClient.
"""
__RCSID__ = "$Id$"
import time
import thread
import DIRAC
from DIRAC.Core.DISET.private.Protocols import gProtocolDict
from DIRAC.FrameworkSystem.Client.Logger import gLogger
from DIRAC.Core.Utilities imp... | Andrew-McNab-UK/DIRAC | Core/DISET/private/BaseClient.py | Python | gpl-3.0 | 26,577 | [
"DIRAC"
] | b9a77ef850520c67dc4f501aef5a933f50433c272c9e0d86d7fafeeed89f2c2d |
# Generated by Django 2.2.2 on 2019-10-24 18:25
from django.db import migrations, models
class Migration(migrations.Migration):
dependencies = [
('foirequest', '0040_auto_20190718_1815'),
]
operations = [
migrations.AlterField(
model_name='foimessage',
name='kind... | stefanw/froide | froide/foirequest/migrations/0041_auto_20191024_2025.py | Python | mit | 555 | [
"VisIt"
] | 95a965d028e3be5f0f3f4d3fd7cab9bd2d5571b29b07b00975f5701c5d2ff19d |
#Just a copy of the version in python 2.5 to be used if it's not available in jython 2.1
"""Simple XML-RPC Server.
This module can be used to create simple XML-RPC servers
by creating a server and either installing functions, a
class instance, or by extending the SimpleXMLRPCServer
class.
It can also be used to hand... | hinesmr/mica | util/pydevd/pysrc/_pydev_SimpleXMLRPCServer.py | Python | apache-2.0 | 21,674 | [
"Brian"
] | dff211b6a48d483cfbf755778feb960d623b403bdb175c0e75fb9fe05843393a |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | chemelnucfin/tensorflow | tensorflow/python/autograph/pyct/transformer_test.py | Python | apache-2.0 | 12,687 | [
"VisIt"
] | 45bd23e26c8df775670ae1f1e59a04a0a5d12d0877d5fae68c74c7d950d06a49 |
import os
import ssl
import sys
import signal
import tornado.web
import tornado.process
import tornado.httpserver
import tornado.autoreload
from DIRAC import gLogger, S_OK
from WebAppDIRAC.Core.HandlerMgr import HandlerMgr
from WebAppDIRAC.Core.TemplateLoader import TemplateLoader
from WebAppDIRAC.Lib.SessionData impo... | DIRACGrid/WebAppDIRAC | src/WebAppDIRAC/Core/App.py | Python | gpl-3.0 | 6,626 | [
"DIRAC"
] | 1d03b271328c20e8b660425565958331da81ba4d1c92d7c00690bd7c177af5b0 |
# ################################################################
#
# Active Particles on Curved Spaces (APCS)
#
# Author: Rastko Sknepnek
#
# Division of Physics
# School of Engineering, Physics and Mathematics
# University of Dundee
#
# (c) 2013, 2014
#
# This program cannot be ... | sknepneklab/SAMoS | utils/InitialAnalysis/dat2vtk.py | Python | gpl-3.0 | 3,308 | [
"ParaView",
"VTK"
] | a684deefcdbf0a86d53de0f83420f4d20599b8a66b9d01866703d68316fe7ee0 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this
# file, You can obtain one at http://mozilla.org/MPL/2.0/.
import datetime
import json
import os
import gzip
import shutil
import stat
from contextlib import contextmanager, clos... | KaiRo-at/socorro | socorro/external/fs/crashstorage.py | Python | mpl-2.0 | 30,495 | [
"VisIt"
] | e3cdc874666c1d6dca23c0ec2d30f6302827a58ddecc8a3753a3c09298d38879 |
from __future__ import division, print_function, absolute_import
import itertools as itr
import numpy as np
def resize_by_factor(im, factor):
"""
Resizes the image according to a factor. The image is pre-filtered
with a Gaussian and then resampled with bilinear interpolation.
This function uses sciki... | amitgroup/amitgroup | amitgroup/image.py | Python | bsd-3-clause | 7,989 | [
"Gaussian"
] | db5f2bf6005a8c3088e090385eabcc71f8d2a2a50d5b478468da7bd1fc092727 |
from Bio import SeqIO, GenBank, AlignIO
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from ete2 import Tree
from collections import Counter
from Bio.Alphabet import IUPAC
from Bio.Blast.Applications import NcbiblastpCommandline as blastp
from mechanize import Browser
import os, glob, re, csv, time, operat... | Van-Doorslaer/PaVE | ORFtools.py | Python | gpl-2.0 | 15,016 | [
"BLAST"
] | 8823ec637b111e59294e93c7cb0f6c712bcbe7621300d71f38699b455844adef |
# Principal Component Analysis Code :
from numpy import mean,cov,double,cumsum,dot,linalg,array,rank,size,flipud
from pylab import *
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import ro... | tapomayukh/projects_in_python | sandbox_tapo/src/skin_related/BMED_8813_HAP/Features/single_feature/best_kNN_PC/cross_validate_objects_kNN_PC_BMED_8813_HAP_scaled_method_II_force.py | Python | mit | 4,363 | [
"Mayavi"
] | 8135744a30120956db2f61b2a883caca77ff7c9ed238ce3bbdca753a9b4cc003 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkXMLUnstructuredGridReader(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | chrisidefix/devide | modules/vtk_basic/vtkXMLUnstructuredGridReader.py | Python | bsd-3-clause | 528 | [
"VTK"
] | 511b34705b42269099009b5a394115a40bf632692d67391976288110a19a1a88 |
import _ExocortexAlembicPython as alembic
import sys
import argparse
# ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ---- ----
# global variables
b_verbose = False
obj_filter = None
typ_filter = None
noo_filter = None
not_filter = None
# ---- ---- ---- -... | Exocortex/ExocortexCrate | Python/samples/filterABC.py | Python | bsd-3-clause | 6,086 | [
"VisIt"
] | d817f87bc803217ef3d6f01c85516b8d0db089bdb6c785023351f45d44674140 |
from fancyimpute import KNN, SimpleFill, IterativeSVD
import pandas as pd
from sklearn.feature_selection import SelectKBest
from sklearn.feature_selection import chi2, f_classif, mutual_info_classif
class Preprocessing:
"""
Contains the functionalities for data standardization, feature selection and missing va... | DEIB-GECO/PyGMQL | gmql/ml/algorithms/preprocessing.py | Python | apache-2.0 | 4,867 | [
"Gaussian"
] | 2b7552a5492bc4d16a2dd533602fa24c702a70319b17249280826b943f2c19fd |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
# CREATED:2015-03-02 11:50:46 by Brian McFee <brian.mcfee@nyu.edu>
'''A python wrapper for rubberband'''
from .pyrb import *
from .version import version as __version__
| bmcfee/pyrubberband | pyrubberband/__init__.py | Python | isc | 218 | [
"Brian"
] | e65adab60171994bc39fe0588e5e81662a2a6bb6ec6f3b48742eb747089e34cb |
"""
NASA Sloan Atlas
----------------
This shows some visualizations of the data from the NASA SDSS Atlas
"""
# Author: Jake VanderPlas <vanderplas@astro.washington.edu>
# License: BSD
# The figure is an example from astroML: see http://astroML.github.com
import numpy as np
from matplotlib import pyplot as plt
from... | nhuntwalker/astroML | examples/datasets/plot_nasa_atlas.py | Python | bsd-2-clause | 1,668 | [
"Galaxy"
] | 1253984ab4f994965b93084c8a3ec7191290245df9c75f308d651768d0e12b33 |
# Orca
#
# Copyright 2005-2008 Sun Microsystems Inc.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your option) any later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/rhythmbox/__init__.py | Python | gpl-3.0 | 1,002 | [
"ORCA"
] | a6dd81a3de3c12a1302eca6b85392e88e4056e29bf291a69e8e232025f9d7cf6 |
"""
Generates a Java class that can map an Android device model String to a
user friendly String.
"""
__author__ = 'tslamic'
__license__ = 'Apache 2.0'
__version__ = '0.0.1'
from datetime import datetime
import string
import time
import os
import re
try:
import requests
except ImportError:
requests = None #... | RyanTech/AndroidDeviceNames | generator/adn.py | Python | apache-2.0 | 9,254 | [
"Galaxy"
] | 5c281d83b69b8d608a71b2adf97966f0f436a6160500376f9f6f05352aba58dc |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import numpy as np
import scipy.signal
import scipy.fftpack
def moving_average(x, window_size, sigma=None):
""" Apply a non-causal moving average filter to signal x. Window size must
be positive and odd. If sigma is None, all samples in the window are
weighted... | oliverlee/antlia | python/antlia/filter.py | Python | bsd-2-clause | 1,723 | [
"Gaussian"
] | 6bfc22a8b0ba98cfa4c421d60058372264166e4eb6669034d3f1c6a92f1a88c9 |
import math
import numbers
import warnings
from enum import Enum
import numpy as np
from PIL import Image
import torch
from torch import Tensor
from typing import List, Tuple, Any, Optional
try:
import accimage
except ImportError:
accimage = None
from . import functional_pil as F_pil
from . import functiona... | PaddlePaddle/models | tutorials/mobilenetv3_prod/Step1-5/mobilenetv3_ref/torchvision/transforms/functional.py | Python | apache-2.0 | 59,290 | [
"Gaussian"
] | 46b1c0359c33b48aa58805cbc3441215b4d23850dc1a3902506528950efaf4d6 |
""" Create and send a combined request for any pending operations at
the end of a job:
* fileReport (for the transformation)
* jobReport (for jobs)
* accounting
* request (for failover)
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_f... | yujikato/DIRAC | src/DIRAC/Workflow/Modules/FailoverRequest.py | Python | gpl-3.0 | 3,723 | [
"DIRAC"
] | 4b56f225b8680cd2bb11e03cac4d0732152527e419b2a3f3af9a36362310f6d1 |
# -*- coding: utf-8 -*-
from __future__ import (absolute_import, division, print_function,
unicode_literals)
from .core import UnitedStates
from workalendar.core import MON
class Alabama(UnitedStates):
"Alabama"
include_confederation_day = True
martin_luther_king_label = "Robert E... | sayoun/workalendar | workalendar/usa/alabama.py | Python | mit | 1,650 | [
"COLUMBUS"
] | a924f3f8bcd7e3c938a972f2b4e8b803b714e59ad82bb123670ff3d4e2e39e5b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# test_recoverstats.py
#
# Copyright 2016 Bruno S <bruno.sanchez.63@gmail.com>
#
import os
import shlex
import subprocess
import sys
sys.path.insert(0, os.path.abspath('..'))
import numpy as np
import matplotlib.pyplot as plt
from astropy.time import Time
from astrop... | toros-astro/ProperImage | drafts/test_varpsf_coadd.py | Python | bsd-3-clause | 6,186 | [
"Gaussian"
] | 445d4ae93b0444482fff2b58a75b93ec86b054f7ef4f7bca4b50d06ea0ee02c2 |
# FermiLib plugin to interface with Psi4
#
# Copyright (C) 2017 ProjectQ-Framework (www.projectq.ch)
#
# This program 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 Licens... | ProjectQ-Framework/FermiLib-Plugin-Psi4 | examples/plotter.py | Python | lgpl-3.0 | 3,559 | [
"Psi4"
] | 8a93bf27bf78c8e805e815a03d15d62e7b0bfd62852dbbee679e6e26683c8232 |
"""
Routines for PDB2PQR
This module contains the protein object used in PDB2PQR and methods
used to correct, analyze, and optimize that protein.
----------------------------
PDB2PQR -- An automated pipeline for the setup, execution, and analysis of
Poisson-Boltzmann electrostatics calc... | MonZop/BioBlender | bin/pdb2pqr-1.6/src/routines.py | Python | bsd-2-clause | 64,840 | [
"Amber",
"CHARMM"
] | 6a69959c731de2267ab86d36b88a9de568d4405e6620bf2b04399ef5eda0b55a |
from trbm_base import TRBMBase
import numpy
import math
class TRBMContinuous(TRBMBase):
def __init__(self, number_visible_units, number_hidden_units, order=1):
self.number_visible_units = number_visible_units
self.number_hidden_units = number_hidden_units
self.order = order
self.vi... | aleksandar-mitrevski/graphical-models | boltzmann_machines/trbm_continuous.py | Python | mit | 12,511 | [
"NEURON"
] | 1eb5586aa3144923110f73f5feafe74ce3f24e3f7c5e0d0152bf5e16d591fcc0 |
import sys
import json
import os
import sqlite3
import re
import subprocess
import shutil
import hashlib
import binascii
import numpy as np
"""
[hash]/
raw/
*stuff*
obj/
[hash].obj (with [hash].html)
[hash].mtl
*images*
[hash].json
"type": which c... | neuroailab/stansim | parsers/digimation_parsing.py | Python | mit | 12,461 | [
"VisIt"
] | 9bf5369163318a82abf5aa0366dfff8ee7f7e8ab1f5bcaa729dedff260b545ea |
#
# Copyright (C) 2017-2019 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... | KaiSzuttor/espresso | testsuite/python/accumulator.py | Python | gpl-3.0 | 2,538 | [
"ESPResSo"
] | f1ab27a5de7152e95ef78d29986b6c8923b39f1665ee86b341322f3548980e6b |
#!/usr/bin/env python
"""
binReads.py <binSize> <bamFilename> <outputFilename>
Author: Tony Papenfuss
Date: Fri 26 Jun 2009 16:17:59 EST
Cumulate all reads into a total count for each bin
"""
import os, sys, math
from optparse import OptionParser
import numpy
import pysam
from srt.useful import progressMessage
de... | PapenfussLab/Srtools | bin/bin_reads.py | Python | artistic-2.0 | 2,466 | [
"pysam"
] | 01f1e478b71b6214db2d24a377da25f49cd52ecac6cb61d7f0bb20f88f49fae9 |
# 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 | deletetournament.py | Python | apache-2.0 | 1,324 | [
"Brian"
] | 1acee8d85f0b4a72fb1bf47ec0267e72c7766df7b3a201af82e5e19d8f0a5b37 |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.