text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
'''
Created on Nov 23, 2011
@author: Mirna Lerotic, 2nd Look Consulting
http://www.2ndlookconsulting.com/
Copyright (c) 2013, Stefan Vogt, Argonne National Laboratory
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the... | MapsPy/MapsPy | henke.py | Python | bsd-2-clause | 27,886 | [
"Avogadro"
] | 8dcd5a5353bfc4e1503b90afdc46d0b124ab7e0a517ffcdad3eddee0cf471e7a |
from math import sqrt, pi
import numpy as np
from gpaw.xc.functional import XCFunctional
from gpaw.sphere.lebedev import Y_nL, weight_n
class LDA(XCFunctional):
def __init__(self, kernel):
self.kernel = kernel
XCFunctional.__init__(self, kernel.name)
self.type = kernel.type
def calc... | ajylee/gpaw-rtxs | gpaw/xc/lda.py | Python | gpl-3.0 | 4,822 | [
"GPAW"
] | cf170391792044baa0abda8c079069591a1b64b9587bf6dc86e408aca1fc5da0 |
# $HeadURL$
"""
DISETSubRequest Class encapsulates a request definition to accomplish a DISET
RPC call
:deprecated:
"""
__RCSID__ = "$Id$"
import commands
from DIRAC.Core.Utilities import DEncode, Time
from DIRAC.Core.Utilities.File import makeGuid
class DISETSubRequest:
###############################... | avedaee/DIRAC | RequestManagementSystem/Client/DISETSubRequest.py | Python | gpl-3.0 | 1,499 | [
"DIRAC"
] | a9520081889a5ee2d811abb1f65f3d925a157f79193c0587ddd3ad8c11cf855a |
__author__ = 'Eden Thiago Ferreira'
class __CaminhosMinimos:
"""Classe base para caminhos minimos ponto a ponto"""
def __init__(self, grafo):
self.grafo = grafo
self.nao_visit = set(self.grafo.pontos)
self.visit = set()
self.dist = {}
self.dist_visit = {}
self.... | edenferreira/Grafo-e-Caminhos-Minimos | caminhos_minimos.py | Python | bsd-2-clause | 3,127 | [
"VisIt"
] | 5a2d91964e093f006bab903608fb576a2b3aa48f8c77fef87e3c0ce5fa46458d |
import re
import requests
from difflib import SequenceMatcher
from coalib.results.Diff import Diff
from coalib.bears.LocalBear import LocalBear
from coalib.bears.requirements.PipRequirement import PipRequirement
from coalib.results.RESULT_SEVERITY import RESULT_SEVERITY
from coalib.results.Result import Result
clas... | chriscoyfish/coala-bears | bears/general/InvalidLinkBear.py | Python | agpl-3.0 | 5,000 | [
"VisIt"
] | 7f2a2ca555c232c4e830c4aac60c6af06caa03435287f2b4987f7b66e0b538fd |
"""Livestreamer extracts streams from various services.
The main compontent of Livestreamer is a command-line utility that
launches the streams in a video player.
An API is also provided that allows direct access to stream data.
Full documentation is available at http://livestreamer.tanuki.se/.
"""
__title__ = "l... | noam09/kodi | script.module.israeliveresolver/lib/livestreamer/__init__.py | Python | gpl-3.0 | 1,313 | [
"Brian"
] | a068a52f49c4f600b4e6361e8590aa27bb97a0203f1348eb0a171f8bc4740e90 |
"""
Provides general packaging handling infrastructure and specific implementations of known packaging formats
All packaging format handlers should extend the PackageHandler class defined in this module.
Packages should then be configured through the PACKAGE_HANDLERS configuration option
"""
from octopus.core import... | JiscPER/jper | service/packages.py | Python | apache-2.0 | 30,281 | [
"Octopus"
] | e0820f5da1b402af9c65b62d1bc717d8f2bdc9174e3a67e8ed5956b019d3a005 |
"""
Student Views
"""
import datetime
import logging
import uuid
import json
import warnings
from collections import defaultdict
from urlparse import urljoin, urlsplit, parse_qs, urlunsplit
from django.views.generic import TemplateView
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
i... | deepsrijit1105/edx-platform | common/djangoapps/student/views.py | Python | agpl-3.0 | 104,572 | [
"VisIt"
] | c3dc7a3f6a41a028be930227a9c7ad3ef94655796911a4dcb71e4089d3b12452 |
# test_moose_thread.py ---
#
# Filename: test_moose_thread.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Thu Mar 8 09:38:02 2012 (+0530)
# Version:
# Last-Updated: Thu Mar 8 15:16:03 2012 (+0530)
# By: Subhasis Ray
# Update #: 162
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary... | BhallaLab/moose | moose-examples/snippets/threading_demo.py | Python | gpl-3.0 | 3,452 | [
"MOOSE"
] | 933e44cb3f6f946965335753fd7647c027fd7ecc23604b1900c02d5a13997ba1 |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 16.3.8
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | adityacs/ansible | lib/ansible/modules/network/avi/avi_applicationprofile.py | Python | gpl-3.0 | 6,304 | [
"VisIt"
] | 8c257b0a99750df025e76afcaf43e5baede30b7b0e17b4d83dfd6511759c5ea5 |
# -*- coding: utf-8 -*-
"""
Created on Tue Oct 6 12:33:23 2015
@author: nouamanelaanait
"""
import warnings, os
import numpy as np
import h5py
import multiprocess as mp
from skimage.morphology import dilation, disk
from scipy.ndimage import gaussian_filter
import cv2
class Corrector(object):
''' This is an Obje... | nlaanait/pyxrim | pyxrim/process/corrections.py | Python | mit | 7,949 | [
"Gaussian"
] | ed0cf79f0a0344f08138ccc76b355fe74fa69b9985501ec539573074d9d50ce3 |
# -*- coding: utf-8 -*-
# Copyright 2022 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-securitycenter | tests/unit/gapic/securitycenter_v1beta1/test_security_center.py | Python | apache-2.0 | 234,437 | [
"Octopus"
] | 6e4d4fb81f9c985cf420e1278b8ae8651497fb07850fa7f18e8329f1ae1d2dae |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/interaction/Tabulated.py | Python | gpl-3.0 | 7,354 | [
"ESPResSo"
] | a4f08f6b3a27742a24b12123d0e4f833f3093321f8d859fe7504f025c012b487 |
# -*- coding: utf-8 -*-
# Copyright (c) 2016-2020 Wintermute0110 <wintermute0110@gmail.com>
#
# 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; version 2 of the License.
#
# This program is distr... | Wintermute0110/plugin.program.advanced.MAME.launcher | resources/mame.py | Python | gpl-2.0 | 403,732 | [
"CRYSTAL"
] | ce4761eac66bac89ccff1e43d56594df0ccb1e290daf89c2683e765d2e1ced4d |
# +
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to... | intel-analytics/BigDL | python/chronos/src/bigdl/chronos/autots/model/auto_prophet.py | Python | apache-2.0 | 12,589 | [
"ORCA"
] | e5dacb2f2fd2c6e6470ee90a5b4018a33c306102755f090a5a4dcce4f0901b00 |
from __future__ import print_function
import os
import Bio
import re
import sys
from Bio import SeqIO
from Bio.Blast import NCBIXML
from Bio import Restriction
from Bio.Restriction import *
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Blast.Appli... | eatingcrispr/VirtualEating | archive/Simulating and generating 3MB Xenopus library/eating.py | Python | apache-2.0 | 37,977 | [
"BLAST"
] | ebe6a961ff3a7d27b400d4e0e2b10fd2ccbbbcafc3349de8b8ab09f7beecfea3 |
import uuid
from Firefly import aliases, logging
from Firefly.automation.triggers import Triggers
from Firefly.const import COMMAND_NOTIFY, SERVICE_NOTIFICATION, TYPE_AUTOMATION, API_ALEXA_VIEW, API_FIREBASE_VIEW, API_INFO_REQUEST
from Firefly.helpers.action import Action
from Firefly.helpers.conditions import Conditi... | Firefly-Automation/Firefly | Firefly/helpers/automation/automation.py | Python | apache-2.0 | 10,789 | [
"Firefly"
] | 230b0ae023ce78b3106ffd06b1d0f942374b0976d2c3183ed86b698753c9c0dc |
#!/usr/bin/env python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://pythonhosted.org/setuptools/easy_install.html
"""
from... | EnviroCentre/jython-upgrade | jython/lib/site-packages/setuptools/command/easy_install.py | Python | mit | 86,129 | [
"VisIt"
] | b50f153b44b27be3f7e26766565448a6d8f491c0793f296ab3bd52204ded969c |
import scipy as sp
import scipy as sp
import scipy.linalg as spla
import numpy as np
from functools import reduce
import pyscf
from pyscf import gto, scf, ao2mo, fci, mp, ao2mo
def myump2(mf):
# As UHF objects, mo_energy, mo_occ, mo_coeff are two-item lists
# (the first item for alpha spin, the second for beta ... | shivupa/pyci | methods/misc/testmp2.py | Python | gpl-3.0 | 1,635 | [
"PySCF"
] | ecd40056eff9d6324e9d3efdae873d6785b39ff24e51a8925b601386d9064b0a |
# Copyright 2020 The LUCI Authors. All rights reserved.
# Use of this source code is governed under the Apache License, Version 2.0
# that can be found in the LICENSE file.
"""Expansion of realms_config.Realm into a flat form."""
import collections
from components.auth.proto import realms_pb2
from components.config ... | luci/luci-py | appengine/auth_service/realms/rules.py | Python | apache-2.0 | 17,117 | [
"VisIt"
] | d6a118ef054ae6ffe9f2f85aac0ec6c8e19f149f11a4a995b9a8fa80ddee50b8 |
import os
from fontbakery.profiles.universal import UNIVERSAL_PROFILE_CHECKS
from fontbakery.checkrunner import Section, INFO, WARN, ERROR, SKIP, PASS, FAIL
from fontbakery.callable import check, disable
from fontbakery.message import Message
from fontbakery.fonts_profile import profile_factory
from fontbakery.constan... | graphicore/fontbakery | Lib/fontbakery/profiles/googlefonts.py | Python | apache-2.0 | 211,482 | [
"VisIt"
] | e11032645ab24b95b50603c74ef18f251281f6ed5bb7174b0388d9727a44bb72 |
"""Support for Konnected devices."""
import asyncio
import hmac
import json
import logging
import voluptuous as vol
from aiohttp.hdrs import AUTHORIZATION
from aiohttp.web import Request, Response
from homeassistant.components.binary_sensor import DEVICE_CLASSES_SCHEMA
from homeassistant.components.discovery import ... | HydrelioxGitHub/home-assistant | homeassistant/components/konnected/__init__.py | Python | apache-2.0 | 17,327 | [
"VisIt"
] | ed44c7f87798a0a340e9a2fc1dda4af004afefad45bb4855da77d8242369ae63 |
# 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 RAnnotationhub(RPackage):
"""Client to access AnnotationHub resources
This package... | LLNL/spack | var/spack/repos/builtin/packages/r-annotationhub/package.py | Python | lgpl-2.1 | 2,334 | [
"Bioconductor"
] | 7b9550c9479a2266278142b93446ee0594e654724930f20d9148e2f3ba0f59a6 |
# -*- coding: utf-8 -*-
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""SPM wrappers for preprocessing data
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
... | carolFrohlich/nipype | nipype/interfaces/spm/preprocess.py | Python | bsd-3-clause | 80,978 | [
"Gaussian"
] | 772eb8788723bf0cb268759c12b38fc57f8e20d7795650a8499f447abc45cf02 |
import os
import shutil
from mdtraj import version
if version.release:
docversion = version.short_version
else:
docversion = 'development'
os.mkdir("docs/_deploy")
shutil.copytree("docs/_build/html", "docs/_deploy/{docversion}"
.format(docversion=docversion))
| swails/mdtraj | devtools/travis-ci/set_doc_version.py | Python | lgpl-2.1 | 286 | [
"MDTraj"
] | 4a6c0242f73801d2a7f951a494e4f4a2a3c06e5fee406b1c68b19d451301dd80 |
from __future__ import print_function
import os
import glob
import argparse
import mdtraj as md
import multiprocessing as mp
from AdaptivePELE.utilities import utilities
def parse_arguments():
desc = "Program that performs simple postprocessing of MD simulations."
parser = argparse.ArgumentParser(description=... | AdaptivePELE/AdaptivePELE | AdaptivePELE/analysis/simple_postprocessing.py | Python | mit | 2,213 | [
"MDTraj"
] | 29bd9de8731f622416c7a524d9a0d27aa274a5107fd5152bd32fa5568176207b |
#==============================================================================
#
# Program: ParaView
# Module: build.py
#
# Copyright (c) Kitware, Inc.
# All rights reserved.
# See Copyright.txt or http://www.paraview.org/HTML/Copyright.html for details.
#
# This software is distributed WITHOUT ANY WARRA... | biddisco/VTK | Web/JavaScript/Minimizer/build.py | Python | bsd-3-clause | 2,063 | [
"ParaView"
] | 120b58d35bc5d948a20cfb1b724450d6acbf59b8f2f223a0742c33a719bfc8e3 |
#!/usr/bin/env python
import wx
import wx.html2 as webview
#----------------------------------------------------------------------
class TestPanel(wx.Panel):
def __init__(self, parent, log, frame=None):
self.log = log
wx.Panel.__init__(self, parent, -1)
self.current = "http://wxPython.or... | dnxbjyj/python-basic | gui/wxpython/wxPython-demo-4.0.1/demo/HTML2_WebView.py | Python | mit | 4,783 | [
"VisIt"
] | 8651332d64ecf753012ae7f65c0e24d81c113705796afeb04b3b299d04fcccec |
# coding: utf-8
# Copyright (c) AiiDA Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides conversion between AiiDA StructureData object and
pymatgen Molecule/Structure objects.
"""
__author__ = "Andrius Merkys"
__copyright__ = "Copyright 2015, AiiDA Development Team"
__versio... | gmatteo/pymatgen | pymatgen/io/aiida.py | Python | mit | 2,320 | [
"pymatgen"
] | a6fcd27489f7f662b2bfe3e4d4fce4aa4d1e6f3f1e38a586bdef26c8f67ef22a |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | jensreeder/scikit-bio | skbio/io/_base.py | Python | bsd-3-clause | 7,311 | [
"scikit-bio"
] | 229642aa135d7426dd6fcb5520291ca039e06f07c6a17dee4fabc06bd2b85589 |
#!/usr/bin/env python3
import argparse
import logging
import os.path
import vtk
import json
import sys
import numpy as np
from vtk.util.numpy_support import vtk_to_numpy as v2n
from vtk.util.numpy_support import numpy_to_vtk as n2v
"""Evaluates a function on a given mesh, using the VTK Calculator."""
"""
This calcula... | precice/aste | src/vtk_calculator.py | Python | gpl-3.0 | 10,995 | [
"Gaussian",
"VTK"
] | 698006bd0e33e0e59f84cb9dea5d9f88495330ffdb56f7eb09c5c912855b639c |
# -*- coding: utf-8 -*-
"""
ChemPy is a Python package useful for solving problems in chemistry.
"""
from ._url import __url__
from ._release import __version__
from .chemistry import (
Substance,
Reaction,
Equilibrium,
Species,
balance_stoichiometry,
mass_fractions,
)
from .reactionsystem imp... | bjodah/aqchem | chempy/__init__.py | Python | bsd-2-clause | 709 | [
"ChemPy"
] | 493fabfa2f95bbb1861f45cfa2856a25087aaf4ad9e613edbf1179a3cb4f6c00 |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2015, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This progra... | ywcui1990/nupic.research | htmresearch/frameworks/utils/param_finder.py | Python | agpl-3.0 | 12,312 | [
"Gaussian"
] | 8fdad3b776081a70d71bec36bba028eb632bd8cbbf4084974b8b3044cec1bdcf |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Works for Abinit
"""
import os
import shutil
import time
import abc
import collections
import numpy as np
import copy
from monty.collections import AttrDict
from monty.itertools import chunks
from monty.fu... | montoyjh/pymatgen | pymatgen/io/abinit/works.py | Python | mit | 74,870 | [
"ABINIT",
"Gaussian",
"NetCDF",
"pymatgen"
] | 734240432f475c74243771425e3b029b03a57cf0bc57061cae1868125ac93366 |
__all__ = ['fsvd']
import numpy as np
def fsvd(A, k, i, usePowerMethod=False):
"""
FSVD Fast Singular Value Decomposition
[U,S,V] = FSVD(A,k,i,usePowerMethod) computes the truncated singular
value decomposition of the input matrix A up to rank k using i levels of
Krylov method as given in [1], p... | aasensio/pyiacsun | pyiacsun/linalg/fsvd.py | Python | mit | 3,055 | [
"Gaussian"
] | 59f7c6fe94424767cc9c1cfdc57c6cc68a77191b9bde51c09ad9a93b0707f171 |
import unicodedata
import numpy as np
from .. import conventions, Variable
from ..core import ops
from ..core.pycompat import basestring, unicode_type, OrderedDict
# Special characters that are permitted in netCDF names except in the
# 0th position of the string
_specialchars = '_.@+- !"#$%&\()*,:;<=>?[]^`{|}~'
# ... | cpaulik/xray | xray/backends/netcdf3.py | Python | apache-2.0 | 4,438 | [
"NetCDF"
] | ba82c14dcc41ab9b2972d26155885a5e50d1b8d9a19731431dd1a6bba0e4cdde |
#!/usr/bin/env python
#
# $File: genoStru.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/genoStru.py | Python | gpl-2.0 | 1,769 | [
"VisIt"
] | 4266a0bfbe28ca561d183b13619078b3c273a0645fc13115d9ccd389c34f8d3e |
from sympy import (meijerg, I, S, integrate, Integral, oo, gamma,
hyperexpand, exp, simplify, sqrt, pi, erf, sin, cos,
exp_polar, polygamma, hyper, log, expand_func)
from sympy.integrals.meijerint import (_rewrite_single, _rewrite1,
meijerint_indefinite, _inflate_g, _creat... | AunShiLord/sympy | sympy/integrals/tests/test_meijerint.py | Python | bsd-3-clause | 27,164 | [
"Gaussian"
] | 27c46b3a95be5945fe9223f22e53f03c1c55c4b84c24cf1318e46555069d3813 |
"""
Default Django settings. Override these with settings in the module pointed to
by the DJANGO_SETTINGS_MODULE environment variable.
"""
# This is defined here as a do-nothing function because we can't import
# django.utils.translation -- that module depends on the settings.
def gettext_noop(s):
return s
####... | elena/django | django/conf/global_settings.py | Python | bsd-3-clause | 22,349 | [
"VisIt"
] | 0b431190b591f2546741b5958e2156c3795765292f9c027b3ed261979336757f |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | sirkubax/ansible | lib/ansible/constants.py | Python | gpl-3.0 | 16,496 | [
"Galaxy"
] | ffa8d5acb6f67ee4f907c96a5133d30ac56bb97dfeee699b94d5cf4a278f0d7e |
#! /usr/bin/python
# Copyright (C) 2010-2021 ABINIT group
#
# Written by Matthieu Verstraete in python (compatible v1.9).
# This is free software, and you are welcome to redistribute it
# under certain conditions (GNU General Public License,
# see ~abinit/COPYING or http://www.gnu.org/copyleft/gpl.txt).... | abinit/abinit | scripts/post_processing/phondisp2abi.py | Python | gpl-3.0 | 4,163 | [
"ABINIT",
"VASP",
"phonopy"
] | b226caa3976f266c68454ecdf65435f015773d7234feecd55c72d013d6c58f82 |
r"""
Details about the continum and numerical model equations can be found on:
Agnaou, M., Sadeghi, M. A., Tranter, T. G., & Gostick, J. (2020).
Modeling transport of charged species in pore networks: solution of the
Nernst-Planck equations coupled with fluid flow and charge conservation
equations. Computers & Geoscie... | PMEAL/OpenPNM | scripts/example_transient_nernst_planck.py | Python | mit | 4,890 | [
"ParaView",
"VTK"
] | dcd82c179116c0a52db429531f3cd270b9fe191805e9fe75996f585249603248 |
from __future__ import print_function
import matplotlib
import numpy as np
import copy
import re
import warnings
from astropy import log
from astropy import units as u
from six.moves import xrange
from six import string_types
from ..config import mycfg
from ..config import ConfigDescriptor as cfgdec
from . import uni... | pyspeckit/pyspeckit | pyspeckit/spectrum/fitters.py | Python | mit | 94,508 | [
"Gaussian"
] | 072e02984ff07a15d4cbf5f32f382096954104971d069686516a26cbc430a04b |
"""Random variable generators.
integers
--------
uniform within range
sequences
---------
pick random element
pick random sample
generate random permutation
distributions on the real line:
------------------------------
uniform
... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-3.0/Lib/random.py | Python | mit | 25,561 | [
"Gaussian"
] | 8cc9cf2fd19d5c8a9c02c24db5ca6b1fb459d6ac301e398cc09e1e1f3103bb60 |
# Copyright 2011 Rackspace
# Copyright (c) 2011 X.commerce, a business unit of eBay Inc.
# Copyright 2013 IBM Corp.
# 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
#
# ... | scripnichenko/nova | nova/tests/unit/network/test_manager.py | Python | apache-2.0 | 167,629 | [
"FEFF"
] | 9a43618bd50be780cd537dd1790e051c3f2d14d76784830a9ac193a7fa3de923 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
# Released under t... | MDAnalysis/mdanalysis | package/MDAnalysis/analysis/legacy/__init__.py | Python | gpl-2.0 | 1,837 | [
"MDAnalysis"
] | ba00d652dd0aa3d03202027eb0dd2dc1327f6ed5983d0a077569062fc3945873 |
# !!! This uses the https://newsapi.org/ api. TO comply with the TOU
# !!! we must link back to this site whenever we display results.
import json
import requests
import webbrowser
from colorama import Fore
from plugin import plugin, require
@require(network=True)
@plugin('news')
class News:
def __init__(self):
... | sukeesh/Jarvis | jarviscli/plugins/news.py | Python | mit | 10,494 | [
"VisIt"
] | d0bc37c58988c4a132db23acd03e941f24b0b425f725a93739ad929e1245247d |
""" Summary plots of SHAP values across a whole dataset.
"""
from __future__ import division
import warnings
import numpy as np
from scipy.stats import gaussian_kde
try:
import matplotlib.pyplot as pl
except ImportError:
warnings.warn("matplotlib could not be loaded!")
pass
from ._labels import labels
fro... | slundberg/shap | shap/plots/_violin.py | Python | mit | 23,938 | [
"Gaussian"
] | e50a9b331d35215f602a0fce7ccbf405b99d6a2bf9c9b6cff668d18e9b1887b0 |
# ============================================================================
#
# 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/view/controls/delegates/datetimedelegate.py | Python | gpl-2.0 | 2,386 | [
"VisIt"
] | 49083c3d5f8ee815747f3f1083d6fc6346d4d73f62bf567036d79aef5d39cb1e |
# 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... | vthorsteinsson/tensor2tensor | tensor2tensor/mesh_tensorflow/mtf_image_transformer.py | Python | apache-2.0 | 14,371 | [
"MOE"
] | 6b52b8ff8a973e809ca8f9178d3e26455d50524650dc4f05bee87e0f7caf807f |
"""Support for Ecobee binary sensors."""
from homeassistant.components.binary_sensor import (
BinarySensorDevice,
DEVICE_CLASS_OCCUPANCY,
)
from .const import DOMAIN, ECOBEE_MODEL_TO_NAME, MANUFACTURER, _LOGGER
async def async_setup_platform(hass, config, async_add_entities, discovery_info=None):
"""Old ... | joopert/home-assistant | homeassistant/components/ecobee/binary_sensor.py | Python | apache-2.0 | 4,119 | [
"VisIt"
] | 95fc81af5ea087653234c8c329ea158b41b7eb8fd53312a503c04383755bd3a5 |
#!/usr/bin/env python
"""
@package npt2
*** This code is for the new CUDA platform! ***
NPT simulation in OpenMM. Runs a simulation to compute bulk properties
(for example, the density or the enthalpy of vaporization) and compute the
derivative with respect to changing the force field parameters.
The basic idea is... | kyleabeauchamp/DBayes | ommfb/targets/wat-liquid/npt.py | Python | gpl-2.0 | 54,693 | [
"Gaussian",
"OpenMM",
"TINKER"
] | e60a5eb81266297fab24ae82c89e2e437afc3c307cecc3343e8f7c48d1ff37df |
# -*- coding: utf-8 -*-
"""
This module implements the GenNetwork class, which implements generic network
logic.
"""
from neuron import h
from ouropy.gendendrite import GenDendrite
import numpy as np
class GenNeuron(object):
"""This is the model of a generic neuron.
Attributes
----------
soma - nrn.... | danielmuellernai/ouropy | genneuron.py | Python | mit | 9,082 | [
"NEURON"
] | 94ef536f3b5f82573bf92b90e15d459e69c75706654ee5729d1c0e981bea2b5b |
#!/usr/bin/env python
"""
Introduces velocities/kinetic energy in a system, to match a given
temperature (in Kelvin). Equivalent to an NVT equilibration with
position restraints on non-solvent heavy atoms. Lipid bilayers
are restrained on phosphate atoms in the Z dimension only.
Raises the temperature of the system g... | csblab/md_scripts | openmm/amberff/heatSystem.py | Python | mit | 10,453 | [
"Amber",
"OpenMM"
] | 79f2739d05fb12369648f25f253a8dcf15e383001a3accb5d6ee9163ea4f0668 |
#!/usr/bin/env python
import numpy as np
from gpaw.mpi import world
from gpaw.blacs import BlacsGrid, Redistributor
from gpaw.utilities import compiled_with_sl
def test(comm, M, N, mcpus, ncpus, mb, nb):
grid0 = BlacsGrid(comm, 1, 1)
desc0 = grid0.new_descriptor(M, N, M, N, 0, 0)
A_mn = desc0.zeros(dtype... | ajylee/gpaw-rtxs | gpaw/test/parallel/blacsdist.py | Python | gpl-3.0 | 2,069 | [
"GPAW"
] | 084a7e7c7540a8607af2a16057e1f72bc497c7a0d847a367cd9612e20abea20f |
from flask import Flask, jsonify, render_template, request
import numpy as np
import nest
import os
import json
import anyjson
app = Flask(__name__)
def prep(data):
return map(lambda x: {'x':x[0], 'y':x[1]}, zip(*data))
@app.template_filter('neurons')
def neurons_filter(nodes):
return filter(lambda node: 'g... | babsey/nest-webapp | multiple_neurons_sd.py | Python | mit | 3,814 | [
"NEURON"
] | ed1557490df599e488d3109e24c57273c708aaabde89a3784917df2e450ee17f |
# ----------------------------------------------------------------------------------------------------
#
# Copyright (c) 2018, 2019, 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... | graalvm/mx | mx_native.py | Python | gpl-2.0 | 27,500 | [
"VisIt"
] | 5475b8977bec7b64bffe933f769c48c6c6e5087dbc0225c5cb77ce54df97704e |
#!/usr/bin/env python
"""
This code demonstrates some of the features of authkit.authorize.
Start the server with::
python authorize.py
Then visit http://localhost:8080/ and you should see the output from the
``index()`` method which invites you to try some of the links.
Each method linked to is implement... | nakato/AuthKit | examples/authorize.py | Python | mit | 4,360 | [
"VisIt"
] | 487f3d793ba97502509780a0c76d08ca5f1f653a3f05b48afe0e5f06dd094186 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Module to test fitting routines
"""
# pylint: disable=invalid-name
import os.path
import warnings
from unittest import mock
import pytest
import numpy as np
from numpy import linalg
from numpy.testing import assert_allclose, assert_almost_equal, asser... | dhomeier/astropy | astropy/modeling/tests/test_fitters.py | Python | bsd-3-clause | 45,391 | [
"Gaussian"
] | 7c38a1d4b42230278ad3332e22b7bdce258f4074f01994eec0a315a785550de7 |
# Copyright 2019 Google Inc.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in wr... | google/slo-generator | slo_generator/backends/elasticsearch.py | Python | apache-2.0 | 4,815 | [
"Elk"
] | 9cf59879f76646ee8b7efb395b6ddd1fe9298bdec9ca722eea8cfa1dce018bc9 |
#!/usr/bin/env python
########################################################################
# File : dirac_proxy_get_uploaded_info.py
# Author : Adrian Casajus
########################################################################
"""
Print information about uploaded proxies.
Example:
$ dirac-proxy-get-uplo... | yujikato/DIRAC | src/DIRAC/FrameworkSystem/scripts/dirac_proxy_get_uploaded_info.py | Python | gpl-3.0 | 3,686 | [
"DIRAC"
] | 82ee3e49d7a6aaecad41a0d14f0ab8f402fc5ebf7ea648b6114ebdfa9788cf83 |
class Gro:
"""
the central class in gropy
"""
# -- constructor(s) --
def __init__(self,
system_name=None, num_of_atoms=None,
residue_id=None, residue_name=None,
atom_name=None, atom_id=None,
x=None, y=None, z=None,
v_x=None, v_y=None, v_z=None,
... | caizkun/gropy | gropy/Gro.py | Python | mit | 12,814 | [
"Gromacs"
] | 99a549c857bd1aea642a1bcc77887850da6cfd81b7f3892d2fb229afef7b5f83 |
"""
Single Bubble Model: Natural seep bubble simulations
=====================================================
Use the ``TAMOC`` `single_bubble_model` to simulate the trajectory of a light
hydrocarbon bubble rising through the water column. This script demonstrates
the typical steps involved in running the single bub... | socolofs/tamoc | bin/sbm/seep_bubble.py | Python | mit | 2,477 | [
"NetCDF"
] | 2fdc01202fd1942bc206ada0ee6b78f7867b8b10746204c35df25e818ab2a3cc |
from director import filterUtils
from director import vieweventfilter
from director import visualization as vis
from director import vtkAll as vtk
from director import vtkNumpy as vnp
from director.shallowCopy import shallowCopy
from PythonQt import QtCore
import numpy as np
class PointSelector(object):
'''
U... | patmarion/director | src/python/director/pointselector.py | Python | bsd-3-clause | 4,091 | [
"VTK"
] | f22e883e8d6d72f007e67ecefea9a1409b952e10ab0b2334ac89ff3676543bc9 |
fi_data_key = {'Div':'League Division',
'Date':'Match Date (dd/mm/yy)',
'HomeTeam':'Home Team',
'AwayTeam':'Away Team',
'FTHG':'Full Time Home Team Goals',
'FTAG':'Full Time Away Team Goals',
'FTR':'Full Time Result (H=Home Win, D... | Danie1Johnson/football-index | fi_data_key.py | Python | gpl-2.0 | 8,624 | [
"BWA"
] | 40275fbc20bd23f2ec401f1a2946746ddf40d6f6878e294edc2e5976171b1723 |
#! /usr/bin/env python
import re
import math
import collections
import numpy as np
import time
import operator
from scipy.io import mmread, mmwrite
from random import randint
from sklearn import cross_validation
from sklearn import linear_model
from sklearn.grid_search import GridSearchCV
from sklearn import preproces... | Goodideax/CS249 | predict_combine_5000.py | Python | bsd-3-clause | 14,608 | [
"Gaussian"
] | 7bf46a3ff9906d0406c9b46891dd314cfd7ac7eb750d64a42fc05aee1294e0ed |
from __future__ import print_function
from numpy import *
from rdkit.sping import pid
import math
def DrawSpiral(canvas,startColor,endColor,startRadius,endRadius,nLoops,degsPerSlice=70,degsPerStep=1,
startAngle=0,centerPos=None,dir=1):
if centerPos is None:
centerPos = (canvas.size[0]/2,canvas.siz... | AlexanderSavelyev/rdkit | rdkit/utils/spiral.py | Python | bsd-3-clause | 1,811 | [
"RDKit"
] | 412c5b39540600751448506b08cd0db727378303c5629eff32681e8f0ec5cc7d |
#!/Library/Frameworks/Python.framework/Versions/2.7/bin/python
# USAGE:
# PREAMBLE:
import numpy as np
import sys
import MDAnalysis
psf = sys.argv[1]
traj = sys.argv[2]
# SUBROUTINES:
# MAIN PROGRAM:
nf = open('g_r.dat', 'w')
# set the universe object
u = MDAnalysis.Universe('%s' %(psf), '%s' %(traj), format='... | rbdavid/MolecDynamics | Analysis/RDF/radialdist.py | Python | mit | 2,218 | [
"MDAnalysis"
] | 2b81f395b07c30d1426dc474429e862454fb51a39344858bcc25668394ebeed9 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Functions for Input/Output, including plotting when required.
@author: Antoine Recanati
"""
from __future__ import print_function
import os
import subprocess
import sys
import csv
import matplotlib
matplotlib.use('PS')
import matplotlib.pyplot as plt
import numpy as... | antrec/spectrassembler | ioandplots.py | Python | mit | 7,001 | [
"BWA"
] | e0e118b7cf36f6f7fff45aac6802348181f5f6f9af4f828eb428aa9a70d0472f |
import xml.etree.ElementTree as ET
from os import makedirs
from os import path as os_path
import CppHeaderParser
multiThreadArchicture=True
datatypes = {}
datatypeDeclarations = []
defines = {}
currentFile = ""
prefix = "RPC_" # change prefix inside the header with #pragma RPC prefix EXAMPLE_
# change projectname i... | Crystal-Photonics/RPC-Generator | RPC-gen.py | Python | lgpl-3.0 | 91,328 | [
"CRYSTAL"
] | 8fa88ec3659a01b0a4db30b572d2e113c64277d7d37b409b51d2e4abc77eb9c0 |
"""Support for control of ElkM1 tasks ("macros")."""
from __future__ import annotations
from typing import Any
from homeassistant.components.scene import Scene
from homeassistant.config_entries import ConfigEntry
from homeassistant.core import HomeAssistant
from homeassistant.helpers.entity_platform import AddEntitie... | rohitranjan1991/home-assistant | homeassistant/components/elkm1/scene.py | Python | mit | 1,024 | [
"Elk"
] | c3a777089aac75b4a8580de563fb79695544624dfbcea59f23d288129dd69a37 |
# -*- coding: utf-8 -*-
"""
fem code for practice
check out FEM - Numerical Python pg 690/1311
"""
__author__ = 'Neal Gordon <nealagordon@gmail.com>'
__date__ = '2016-09-06'
from numpy import array, matrix, zeros, linspace, arange
#from matplotlib.pyplot import *
import matplotlib.pyplot as plt... | nagordon/mechpy | mechpy/fem.py | Python | mit | 16,951 | [
"VTK"
] | d01361d104af6dfb3057f5fb70ba4c2763d1bfd2c5b3be58e32e3f076c4b1597 |
"""Implements the hashids algorithm in python. For more information, visit
http://www.hashids.org/. Compatible with Python 2.6, 2.7 and 3"""
import warnings
from functools import wraps
from math import ceil
__version__ = '1.1.0'
RATIO_SEPARATORS = 3.5
RATIO_GUARDS = 12
try:
StrType = basestring
ex... | BioGRID/IMS | operations/database/classes/Hashids.py | Python | lgpl-3.0 | 9,341 | [
"VisIt"
] | 536f54df9a2ad94d51b6d6fdb28925ba70a6e57f3a60fa1f58d6e2952decee41 |
"""
"""
import ast
import operator
from collections import deque
from . import ASTOptimization
class DeadCodeElimination(ASTOptimization):
"""
"""
@property
def name(self) -> str:
return 'Dead code elimination'
@property
def description(self) -> str:
return ''
@prope... | Amper/opyum | opyum/optimizations/dead_code_elimination.py | Python | bsd-3-clause | 2,174 | [
"VisIt"
] | c1cec3f3e0ca88df5d688c4ecd2f1250f14576c4d28575c748b65952c330d823 |
#!/usr/bin/python
import os, subprocess
import textwrap, argparse
if __name__ == '__main__':
argument_parser = argparse.ArgumentParser(
prog='stability_all.py',
formatter_class=argparse.RawDescriptionHelpFormatter,
description=textwrap.dedent('''\
create a graphical functions ... | daniparera/MCR | Senses/analisys/others/stability_all.py | Python | gpl-2.0 | 3,101 | [
"VisIt"
] | dbc46c7ecf2c5ec2d76ce65112b78abd9e70274c5d04198fc6e653156ad4358e |
# Copyright 2009 Brian Quinlan. All Rights Reserved.
# Licensed to PSF under a Contributor Agreement.
__author__ = 'Brian Quinlan (brian@sweetapp.com)'
import collections
import logging
import threading
import time
FIRST_COMPLETED = 'FIRST_COMPLETED'
FIRST_EXCEPTION = 'FIRST_EXCEPTION'
ALL_COMPLETED = 'A... | prefetchnta/questlab | bin/x64bin/python/36/Lib/concurrent/futures/_base.py | Python | lgpl-2.1 | 21,847 | [
"Brian"
] | 63310a112d70f8096759e74908a682137cc1aee8bdbb3aa5eefdbf2fa6d1e541 |
#!/usr/bin/env python
from __future__ import print_function
import vtk
def get_program_parameters():
import argparse
description = 'Add a background image at a render window.'
epilogue = '''
Add a background image to a render window.
'''
parser = argparse.ArgumentParser(description=descri... | lorensen/VTKExamples | src/Python/Images/BackgroundImage.py | Python | apache-2.0 | 3,966 | [
"VTK"
] | 26b1bb6756fb2529346b71f4a716f225fa2fcccdbe13f6a0c64234378425690c |
#!/usr/bin/env python
"""Colored sine wave grating in circular mask"""
############################
# Import various modules #
############################
import VisionEgg
VisionEgg.start_default_logging(); VisionEgg.watch_exceptions()
from VisionEgg.Core import *
from VisionEgg.FlowControl import Presentation, F... | visionegg/visionegg | demo/color_grating.py | Python | lgpl-2.1 | 2,726 | [
"Gaussian"
] | 416fd81fb9303e79ae3f2de2113535e44fe0f2bbbb247709c78f7154453d221c |
# This file is part of DEAP.
#
# DEAP is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as
# published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# DEAP is distributed ... | DEAP/deap | examples/pso/speciation.py | Python | lgpl-3.0 | 6,580 | [
"Gaussian"
] | 17d59a78a80eef3eaa2b0b093197a0b689b3e635ae9dc3d12cb921149c9dde2d |
# Copyright (C) 2020 The Software Heritage developers
# See the AUTHORS file at the top-level directory of this distribution
# License: GNU Affero General Public License version 3, or any later version
# See top-level LICENSE file for more information
from typing import Any, Dict, Iterable, List, Optional
from urllib... | SoftwareHeritage/swh-web-ui | swh/web/common/identifiers.py | Python | agpl-3.0 | 13,679 | [
"VisIt"
] | 3022bdbce8f15d3e48515af3824c418bc59f1fbe8a61f0872a192359fdabc8eb |
"""
"""
#
import time
import pprint
#
#
from models.player import Player
player = Player(player_id=5353462)
player.visit()
| m3talstorm/foe-bot | foe/sabotage.py | Python | mit | 130 | [
"VisIt"
] | 966508da684b206c3288a211888e176db38649af68b60929f27c5323377d1bba |
#!/usr/bin/env python3
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgp... | nuclear-wizard/moose | python/peacock/tests/input_tab/BlockInfo/test_BlockInfo.py | Python | lgpl-2.1 | 5,770 | [
"MOOSE"
] | efb762856e317caa5632081d83bed64d37d58224d30d0ab739776c91404177d6 |
"""
Implementation of Von-Mises-Fisher Mixture models,
i.e. the equaivalent of mixture of Gaussian on the sphere.
Author: Bertrand Thirion, 2010-2011
"""
import numpy as np
from warnings import warn
warn('Module nipy.algorithms.clustering.von_mises_fisher_mixture' +
'deprecated, will be removed',
FutureWar... | arokem/nipy | nipy/algorithms/clustering/von_mises_fisher_mixture.py | Python | bsd-3-clause | 13,461 | [
"Gaussian"
] | dcb2cc35e212403c4f5d3e9c93da1f39f2df9a526e7f09461c3325b5f574609b |
import os
import errno
import threading
import datetime
import tempfile
import shutil
import json
import time
import socket
import re
from copy import deepcopy
from GangaCore.Utility.Config import getConfig
from GangaCore.Utility.logging import getLogger
from GangaCore.Core.exceptions import GangaException
from GangaCo... | ganga-devs/ganga | ganga/GangaDirac/Lib/Utilities/DiracUtilities.py | Python | gpl-3.0 | 12,474 | [
"DIRAC"
] | 59b68a7707869fa816b033a9876c5c435747c67f956a821a6e077f51a423d54a |
"""
This file contains Python code illustrating the creation and manipulation of
vtkTable objects.
"""
from vtk import *
#------------------------------------------------------------------------------
# Some Helper Functions
#------------------------------------------------------------------------------
def add_row_... | naucoin/VTKSlicerWidgets | Examples/Infovis/Python/tables_adv.py | Python | bsd-3-clause | 4,425 | [
"VTK"
] | c0a4a1011fa6242407e0ccbc1a5298b5647ec50b56274a91c9c446dfad0d90e0 |
from __future__ import division, print_function, absolute_import
import numpy as np
from scipy.ndimage import map_coordinates
from dipy.viz.colormap import line_colors
# Conditional import machinery for vtk
from dipy.utils.optpkg import optional_package
# import vtk
# Allow import, but disable doctests if we don't ... | villalonreina/dipy | dipy/viz/utils.py | Python | bsd-3-clause | 14,226 | [
"VTK"
] | 8156a26a95233369593dc9ccfcfce244a7fa75399405a0c13e913b6cdc2dde19 |
from __future__ import unicode_literals
from django.utils.encoding import python_2_unicode_compatible
from django.conf import settings
try:
from django.contrib.contenttypes.fields import GenericForeignKey
except ImportError:
from django.contrib.contenttypes.generic import GenericForeignKey
from django.contrib.c... | rafaelgontijo/Django-facebook-fork | django_facebook/models.py | Python | bsd-3-clause | 23,266 | [
"VisIt"
] | 51ae3e8c048516a18264630b88b66f9c0883c837a8f20e8ce83987209ccf1b48 |
#!/usr/bin/env python
# (C) Copyright IBM Corporation 2004, 2005
# All Rights Reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files (the "Software"),
# to deal in the Software without restriction, including without limitation
# ... | ayoubg/gem5-graphics | Mesa-7.11.2_GPGPU-Sim/src/mapi/glapi/gen/glX_proto_send.py | Python | bsd-3-clause | 32,013 | [
"Brian"
] | c507198c59dde04f4f860693d7bd4b2627dd00a38802aec339967dc8a0c6535a |
import os
import shutil
import unittest
from unittest import TestCase
from pymatgen.io.qchem.inputs import QCInput
from custodian.qchem.handlers import QChemErrorHandler
__author__ = "Samuel Blau, Brandon Woods, Shyam Dwaraknath, Ryan Kingsbury"
__copyright__ = "Copyright 2018, The Materials Project"
__version__ = "... | materialsproject/custodian | custodian/qchem/tests/test_handlers.py | Python | mit | 12,265 | [
"pymatgen"
] | 050a262f80402f11fc10b0f315d2d896ecc5dc61faa102695cf2ad1caf4b1e87 |
"""Shared functionality useful across multiple structural variant callers.
Handles exclusion regions and preparing discordant regions.
"""
import collections
import os
import numpy
import pybedtools
import pysam
import toolz as tz
import yaml
from bcbio import bam, utils
from bcbio.distributed.transaction import fil... | brainstorm/bcbio-nextgen | bcbio/structural/shared.py | Python | mit | 13,904 | [
"pysam"
] | 5502ed98c6cabfcfcd1596536091f54c46e5220c6c83fbf928c39293d8203ca7 |
from PyQt4.QtCore import pyqtSlot, pyqtSignal, pyqtProperty
from PyQt4.QtCore import QAbstractListModel, QModelIndex
from PyQt4.QtCore import Qt, QObject, QUrl, QStringList
from PyQt4.QtGui import QApplication, QWidget, QColor, qRgb
from PyQt4.QtDeclarative import QDeclarativeView
import os
import numpy as np
from ase.... | csmm/multiase | atomsview/atomsview.py | Python | gpl-2.0 | 5,997 | [
"ASE",
"CHARMM",
"LAMMPS"
] | a703fa3fd5905c39f221f53a7d2f764107b69595be7786b687d80ed68806747d |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Accfft(CMakePackage, CudaPackage):
"""AccFFT extends existing FFT libraries for CUDA-enabl... | iulian787/spack | var/spack/repos/builtin/packages/accfft/package.py | Python | lgpl-2.1 | 1,649 | [
"NetCDF"
] | ddc37a5a4b2218533087970461e8e0f6e05027d123dce557826ea11fde305d63 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# This is the module's setup script. To install this module, run:
#
# python setup.py install
#
""" Concurrent logging handler (drop-in replacement for RotatingFileHandler)
Overview
========
This module provides an additional log handler for Python's standard logging
pa... | dsuch/ConcurrentLogHandler | setup.py | Python | apache-2.0 | 10,099 | [
"exciting"
] | 1f15f9cdbc3cc1a6e6b66844f4eaba3825b2201ce39e6c9e39f8d95a1540815c |
#
# Copyright (C) 2018 Susan H. Leung
# All Rights Reserved
#
from rdkit import RDConfig
import os
import sys
import math
from datetime import datetime, timedelta
import unittest
from rdkit import DataStructs
from rdkit import Chem
from rdkit.Geometry import rdGeometry as geom
from rdkit.Chem.rdchem import Atom... | rdkit/rdkit | Code/GraphMol/MolStandardize/Wrap/testMolStandardize.py | Python | bsd-3-clause | 42,058 | [
"RDKit"
] | bd327a8adb4c23d624441b269d2ab227aceec639bfc633c62af454dedf56eff9 |
import ast
from .base import (
BaseAnalyzer, Result, AttributeVisitor, ModuleVisitor, set_lineno,
)
class CallVisitor(ast.NodeVisitor):
"""
Collects all usable attributes and names inside function call.
"""
def __init__(self):
self.names = set()
def visit_Attribute(self, node):
... | alfredhq/djlint | djlint/analyzers/render_to_response.py | Python | isc | 2,433 | [
"VisIt"
] | 0b96366cecec748522c7ab24cc50cfd3efed19496b273101404774b184a187d2 |
#!/usr/bin/env python
"""
Get the given file replica metadata from the File Catalog
"""
import os
from DIRAC import exit as DIRACExit
from DIRAC.Core.Base.Script import Script
@Script()
def main():
# Registering arguments will automatically add their description to the help menu
Script.registerArgument(("Loc... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_replica_metadata.py | Python | gpl-3.0 | 1,780 | [
"DIRAC"
] | 8e9aa41623ff193777d8579aa5ca25b5f3945c973fda1ea8833ba5b41d25c914 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-install-agent
# Author : Ricardo Graciani
########################################################################
"""
Do the initial installation and configuration of a DIRAC agent
"""
__RCSID_... | rajanandakumar/DIRAC | Core/scripts/dirac-install-agent.py | Python | gpl-3.0 | 3,506 | [
"DIRAC"
] | 8cb9ccf5b1178e0ef935f4ecab5ff4a946d5a93a72f15278350668693dfa224a |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
RANGE = 150
MAX_ITERATIONS_1 = RANGE
MAX_ITERATIONS_2 = RANGE
XRAD = 200
YRAD = 200
mandelbrot1 = vtk.vtkImageMandelbrotSource()
mandelbrot1.SetMaximumNumberOfIterations... | hlzz/dotfiles | graphics/VTK-7.0.0/Imaging/Core/Testing/Python/TestMapToWindowLevelColors.py | Python | bsd-3-clause | 933 | [
"VTK"
] | 308b65b1b3c3c05287b7c5e806184c7481c2c052d9d055485d7c3854ac63f6e0 |
import moose
import rdesigneur as rd
rdes = rd.rdesigneur(
stimList = [['soma', '1', '.', 'inject', '(t>0.1 && t<0.2) * 2e-8' ]],
plotList = [['soma', '1', '.', 'Vm', 'Soma membrane potential']]
)
rdes.buildModel()
moose.reinit()
moose.start( 0.3 )
rdes.display() | BhallaLab/moose-examples | tutorials/Rdesigneur/ex2.0_currentPulse.py | Python | gpl-2.0 | 272 | [
"MOOSE"
] | 594d0c3a81bc2c4d25e1529d7f47b7fc172affbe8f84d486746c3265ef4e4d0c |
#
# This file is a part of the normalize python library
#
# normalize is free software: you can redistribute it and/or modify
# it under the terms of the MIT License.
#
# normalize is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FI... | hearsaycorp/normalize | normalize/visitor.py | Python | mit | 28,877 | [
"VisIt"
] | 0c7770956b31a9ae31831898b06b22973853c25fadadeb0a077a2a87bdb85488 |
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