text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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""" Update all the Transformation counters, to speed up the production monitoring page loading
It requires the definition of Operations section Transformation/TasksStates and Transformation/FilesStates
Those are also used to define the columns in the TransformationCounters table
"""
from DIRAC ... | avedaee/DIRAC | TransformationSystem/Agent/UpdateTransformationCounters.py | Python | gpl-3.0 | 4,276 | [
"DIRAC"
] | a7196319cf30011023bd7f6a7ea2d87623aa9ced68d6a0f3ff076f8865a9662d |
# Lint as: python2, python3
# Copyright 2018 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
... | arborh/tensorflow | tensorflow/tools/compatibility/tf_upgrade_v2.py | Python | apache-2.0 | 101,992 | [
"Gaussian",
"VisIt"
] | 5d26aa4eae51981ba253fed74ff8714371536be6cad6b8c0d0d5c5fab1a52229 |
import warnings
from sympy import Basic, Symbol, Integer
from sympy.core import sympify
from sympy.core.basic import S, C
from sympy.polys import Poly, roots
from sympy.simplify import simplify
from sympy.utilities import any
# from sympy.printing import StrPrinter /cyclic/
import random
class NonSquareMatrixExcept... | jbaayen/sympy | sympy/matrices/matrices.py | Python | bsd-3-clause | 64,090 | [
"DIRAC",
"Gaussian"
] | 6c1b2e82fca5b16e9f5102e1b3d8bd856fce09876b6148d942e7574be21e0b44 |
"""
Test helper functions and base classes.
"""
import functools
import io
import json
import os
import sys
from datetime import datetime
from unittest import SkipTest, TestCase
import requests
import six
from bok_choy.javascript import js_defined
from bok_choy.page_object import XSS_INJECTION
from bok_choy.promise ... | msegado/edx-platform | common/test/acceptance/tests/helpers.py | Python | agpl-3.0 | 17,362 | [
"VisIt"
] | 029775909dc29cfa6b2bf80b8beddc9c532b29bcc152c739351bcaa8f344ea54 |
from scipy import stats
import numpy as np
import matplotlib.pyplot as plt
import matplotlib
import pickle
import scipy
from astropy.io import fits
from astropy.table import Table
from astropy.coordinates import SkyCoord
from astropy.time import Time
# read data:
pkl_file = open(
'/Users/caojunzhi/Desktop/NY... | peraktong/Cannon-Experiment | compare/0425_compare_nick_us_scatter.py | Python | mit | 10,290 | [
"VisIt"
] | a5284932c97133aabf0aa46f8e185d7417538608f33967f49478804fa2abc544 |
#
# The Python Imaging Library.
# $Id$
#
# standard filters
#
# History:
# 1995-11-27 fl Created
# 2002-06-08 fl Added rank and mode filters
# 2003-09-15 fl Fixed rank calculation in rank filter; added expand call
#
# Copyright (c) 1997-2003 by Secret Labs AB.
# Copyright (c) 1995-2002 by Fredrik Lundh.
#
# See t... | kenshay/ImageScript | ProgramData/SystemFiles/Python/Lib/site-packages/PIL/ImageFilter.py | Python | gpl-3.0 | 15,352 | [
"Gaussian"
] | c68628464b81835adf457bde8caad793ab6399e40acd01f2157ec4a014283f33 |
#
# Copyright (C) 2013-2018 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... | mkuron/espresso | samples/lj_liquid_structurefactor.py | Python | gpl-3.0 | 6,427 | [
"ESPResSo"
] | 599f3c938c20d4a293b8124b9c71e458dfb363aaf61d848ba2723e3377458f51 |
# filename: EPIC2Datetime.py
r'''Module to convert PMEL-EPIC timeword to a python datetime
Modifications
-------------
'''
import datetime
from netCDF4 import date2num
__author__ = 'Shaun Bell'
__email__ = 'shaun.bell@noaa.gov'
__created__ = datetime.datetime(2016, 07, 21)
__modified__ = datetime... | shaunwbell/FOCI_Analysis | ReanalysisRetrieval/calc/EPIC2Datetime.py | Python | mit | 6,382 | [
"NetCDF"
] | 6c5d04daf9c43b837530efab7ddc37b700eca917a9455ce03d8dcd9004d3d27d |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2005-2007 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 Softw... | andrebellafronte/stoq | stoqlib/domain/profile.py | Python | gpl-2.0 | 5,202 | [
"VisIt"
] | 7a7686c720aa610477653a6167b28d088735e2f39b024911790905d567359858 |
#!/usr/local/bin python
# -*- coding: utf-8 -*-
from SOM.Model import SOM, run
from SOM import logger
from SOM import Map
from SOM import Coefficients as coef
from map_eval import map_eval
import RPSOM_config
import numpy as np
import copy
class RPSOM:
def __init__ (self, epochs=10
, map_size_x=10, map_size_y... | kinect110/RPSOM | src/RPSOM/Model.py | Python | mit | 11,417 | [
"Gaussian"
] | 236d549efbd26663a0e0fe00cbc8572e199bc36b8e38e254676f4d8bf0cb9ca3 |
"""
Classes related to parameter validation.
"""
import os, re, logging
from elementtree.ElementTree import XML
from galaxy import model
log = logging.getLogger( __name__ )
class LateValidationError( Exception ):
def __init__( self, message ):
self.message = message
class Validator( object ):
"""
... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/tools/parameters/validation.py | Python | gpl-3.0 | 14,662 | [
"Galaxy"
] | add5fff85583f893bc5a113f3664a4c2384fb1a0b92c476a13e7853d80c2ed10 |
from common import HTTPBruteModule, ModuleMetadata, WebRequests, Modules
class dexter_v1(HTTPBruteModule):
def __init__(self):
md = ModuleMetadata(
module_name="dexter_v1",
bot_name="Dexter v1",
description="Point of sale malware designed to extract credit card informat... | bwall/BAMF | bamfbrute/modules/dexter_v1.py | Python | mit | 1,399 | [
"Brian"
] | 7c954904fc1aa872a951dd81aa00defc1d32854aeb26b330276ac479aa7a9d5a |
# (c) 2014, Brian Coca, Josh Drake, et al
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
... | krishnazure/ansible | v1/ansible/cache/redis.py | Python | gpl-3.0 | 3,477 | [
"Brian"
] | 2a25f363a3f71fd09c4ab1f7c1a484a3309e4d60d33c2157cc497d8e5e74f12d |
"""
Stratified Plume Model: Lake simulation
========================================
Use the ``TAMOC`` `stratified_plume_model` to simulate a lake aeration plume.
This script demonstrates the typical steps involved in running the single
bubble model with reactive (dissolving) particles.
This simulation uses the am... | socolofs/tamoc | bin/spm/lake_bub.py | Python | mit | 5,163 | [
"NetCDF"
] | 3dabe90458d3068c77a1326fc700b04d1a8333f7885a005568f9ddc56fa7833e |
""" Module for galaxies related to FRBs
"""
from __future__ import print_function, absolute_import, division, unicode_literals
import numpy as np
import os
import warnings
import glob
from pkg_resources import resource_filename
from astropy.coordinates import SkyCoord
from astropy import units
from astropy.table im... | FRBs/FRB | frb/galaxies/frbgalaxy.py | Python | bsd-3-clause | 29,238 | [
"Galaxy"
] | 54e257451e028a0978258e9f54f4911eb743706e7430bf410b02a1addd3c938e |
# ===============================================================================
# Copyright (C) 2010 Diego Duclos
#
# This file is part of pyfa.
#
# pyfa 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... | bsmr-eve/Pyfa | eos/db/saveddata/loadDefaultDatabaseValues.py | Python | gpl-3.0 | 14,554 | [
"Jaguar"
] | 4ccb926820321b027478d46d15147255b1edb1e256d4147f80865f8e7fc0bab7 |
"""
This module contains tests for tofu.geom in its structured version
"""
# Built-in
import os
import sys
import warnings
import itertools as itt
# Standard
import numpy as np
import scipy.constants as scpct
import matplotlib.pyplot as plt
# tofu-specific
from tofu import __version__
import tofu as tf
import tofu.... | ToFuProject/tofu | tofu/tests/tests04_spectro/test_01_fit12d.py | Python | mit | 29,357 | [
"CRYSTAL"
] | 3788375c87c9817890a4dd23e8627c4414ed724bf712f8fe7b61597afde8fb0f |
import click
from parsec.cli import pass_context, json_loads
from parsec.decorators import custom_exception, json_output
@click.command('resume_job')
@click.argument("job_id", type=str)
@pass_context
@custom_exception
@json_output
def cli(ctx, job_id):
"""Resume a job if it is paused.
Output:
dict containin... | galaxy-iuc/parsec | parsec/commands/jobs/resume_job.py | Python | apache-2.0 | 485 | [
"Galaxy"
] | ec2f14e8372ba62b892a8da8044ce4e33c3235e32807894990c8b405ea0afa3d |
################################# LICENSE ##################################
# Copyright (c) 2009, South African Astronomical Observatory (SAAO) #
# All rights reserved. #
# #
# Redistribu... | saltastro/pysalt | lib/saltfit.py | Python | bsd-3-clause | 12,791 | [
"Gaussian"
] | 413d7a66881d46f75eb50a50fd6117ef713e3c08211eca98a3edc86c41ea7cf7 |
import catmap
from catmap.model import ReactionModel
from catmap import ReactionModelWrapper
import numpy as np
import mpmath as mp
from ase.atoms import string2symbols
class SolverBase(ReactionModelWrapper):
def __init__(self,reaction_model=None):
"""
Class for `solving' for equilibrium coverages ... | mhoffman/catmap | catmap/solvers/solver_base.py | Python | gpl-3.0 | 11,172 | [
"ASE"
] | 98ecbd332858c523cd2a93af7078077caf2280ee03b7474c3fe225a1867ea1c0 |
# -*- coding: utf-8 -*-
#GSASIIobj - data objects for GSAS-II
########### SVN repository information ###################
# $Date: 2018-07-13 02:37:20 +0300 (Fri, 13 Jul 2018) $
# $Author: toby $
# $Revision: 3469 $
# $URL: https://subversion.xray.aps.anl.gov/pyGSAS/trunk/GSASIIobj.py $
# $Id: GSASIIobj.py 3469 2... | AntonGagin/GSAS_USE | patchSystErrors/originalOld/GSASIIobj.py | Python | gpl-3.0 | 135,881 | [
"CRYSTAL",
"Gaussian"
] | 7fb224312ad1869d1603828ba306f386b21cdf9f58ea4a296385020615249333 |
from abc import abstractmethod
import logging
from typing import List, Optional
import numpy as np
from rdkit import Chem
from guacamol.utils.chemistry import smiles_to_rdkit_mol
from guacamol.score_modifier import ScoreModifier, LinearModifier
from guacamol.utils.math import geometric_mean
logger = logging.getLogge... | BenevolentAI/guacamol | guacamol/scoring_function.py | Python | mit | 8,273 | [
"RDKit"
] | aa7edd8dcabd98a3799c5896da23e1ccf31e7dbd6dc7b4284c592db9a535207e |
from Components.ActionMap import ActionMap, HelpableActionMap, NumberActionMap
from Components.AVSwitch import AVSwitch
from Components.Button import Button
from Components.ConfigList import ConfigList, ConfigListScreen
from Components.config import ConfigText, ConfigInteger, ConfigSelection, ConfigSubList, ConfigS... | Lululla1/XCplugin | src/plugin.py | Python | gpl-2.0 | 138,271 | [
"VisIt"
] | 9d1dee4ede0a2169442dc6de8b8a480c4a36a21bd7594e4e7102ed56c16b9ad2 |
# -*- coding: utf-8 -*-
"""
==================================
Regularized OT with generic solver
==================================
Illustrates the use of the generic solver for regularized OT with
user-designed regularization term. It uses Conditional gradient as in [6] and
generalized Conditional Gradient as propos... | aje/POT | examples/plot_optim_OTreg.py | Python | mit | 2,940 | [
"Gaussian"
] | 905217e2b7ffff93c4576136605a30f1de4749f6f3239a206572bd33a572c0af |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/e2-openwbif | plugin/controllers/views/web/mediaplayerload.py | Python | gpl-2.0 | 5,214 | [
"VisIt"
] | 998b4dbea025894590e819ff23b0dc9acd89c2c9936bdeb35e2edd4079a7fe7b |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | RackSec/ansible | lib/ansible/modules/network/avi/avi_analyticsprofile.py | Python | gpl-3.0 | 27,872 | [
"VisIt"
] | 0eb940659e5d6bf99ce4195d9893c0cce640407183f131877e595210ac85d66d |
#! /usr/bin/python
# coding=utf-8
from setuptools import setup, find_packages
if __name__ == '__main__':
RELEASE = "1.3.0"
with open("README.rst") as summary:
LONG_DESCRIPTION = summary.read()
setup(name='RotamerConvolveMD',
version=RELEASE,
description='Analysis of spin labe... | MDAnalysis/RotamerConvolveMD | setup.py | Python | gpl-2.0 | 2,408 | [
"MDAnalysis"
] | 0b0f0d79e4f445545f2a75aa09247cfc9d405701922f7b9709df6282a4133978 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | EmreAtes/spack | var/spack/repos/builtin/packages/abinit/package.py | Python | lgpl-2.1 | 7,252 | [
"ABINIT",
"NetCDF"
] | dc5317f82f39f3b5ee2d59070750153c0ca9924f5ce4bb554cdd3a333e22ca9f |
"""
Tests for geography support in PostGIS
"""
import os
from unittest import skipIf, skipUnless
from django.contrib.gis.db import models
from django.contrib.gis.db.models.functions import Area, Distance
from django.contrib.gis.measure import D
from django.db import connection
from django.db.models.functions import Ca... | blighj/django | tests/gis_tests/geogapp/tests.py | Python | bsd-3-clause | 7,024 | [
"VisIt"
] | d605c231b0f58c4db02590389e181149cd7a7b8a696e5e2bfb176ccc3cf61729 |
import Tools.HTML
if __name__ == "__main__":
import sys,os
selfname = sys.argv[0]
full_path = os.path.abspath(selfname)[:]
last_slash = full_path.rfind('/')
dirpath = full_path[:last_slash] + '/..'
print("Append to PYTHONPATH: %s" % (dirpath))
sys.path.append(dirpath)
import re,logging
fro... | talipovm/terse | terse/Interface/NBO.py | Python | mit | 13,949 | [
"Gaussian"
] | b8ede2684c9caa5ddbb419fa422be116ade50e7be8a433676dd274b9e630f7c4 |
# GromacsWrapper config.py
# Copyright (c) 2009-2011 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
"""
:mod:`gromacs.config` -- Configuration for GromacsWrapper
==========================================================
The... | CTCNano/GromacsWrapper | gromacs/config.py | Python | gpl-3.0 | 25,118 | [
"Gromacs"
] | 9387fc0131323055bafe03f14345376cef9862bf83f61a825e6f16ba912f7c5c |
###############################################################################
##
## Copyright (C) 2011-2014, NYU-Poly.
## Copyright (C) 2006-2011, University of Utah.
## All rights reserved.
## Contact: contact@vistrails.org
##
## This file is part of VisTrails.
##
## "Redistribution and use in source and binary for... | Nikea/VisTrails | scripts/dist/mac/setup.py | Python | bsd-3-clause | 3,878 | [
"VTK"
] | c7121ed03d18ef3ea2f1e61216712d1b6bfe0e6b47bb67a39af7c416b340126d |
#!/usr/bin/env python
########################################################################
# File : dirac-wms-job-parameters
# Author : Stuart Paterson
########################################################################
"""
Retrieve parameters associated to the given DIRAC job
"""
__RCSID__ = "$Id$"
im... | andresailer/DIRAC | Interfaces/scripts/dirac-wms-job-parameters.py | Python | gpl-3.0 | 1,224 | [
"DIRAC"
] | a8bebb049bd3be01539c372b599b36b903c2fa167f06adc80248c3f768f4f64c |
#!/usr/bin/python
# -*- coding: utf-8 -*-
################################################################################
#
# RMG - Reaction Mechanism Generator
#
# Copyright (c) 2002-2010 Prof. William H. Green (whgreen@mit.edu) and the
# RMG Team (rmg_dev@mit.edu)
#
# Permission is hereby granted, free of c... | enochd/RMG-Py | rmgpy/data/solvation.py | Python | mit | 36,641 | [
"VisIt"
] | a5be378a0574ba0e6e70468d978583001bf74d8fe63399734ddea0e370771211 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
ANSIB... | alxgu/ansible | lib/ansible/modules/network/avi/avi_wafpolicy.py | Python | gpl-3.0 | 5,690 | [
"VisIt"
] | 2b6768738b2a6327780330a3fcae1e51621a3457d431cb302b10ab08c4f5ae2b |
# coding: utf-8
from __future__ import unicode_literals, division, print_function
import os.path
import collections
from tempfile import mkdtemp
from pymatgen.util.testing import PymatgenTest
from pymatgen.io.abinitio import *
_test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..", "..",
... | rousseab/pymatgen | pymatgen/io/abinitio/tests/test_works.py | Python | mit | 1,336 | [
"pymatgen"
] | 9e2e7f1699fb33e6004af1b2ea551cb41fda25a48a6b6954a7cb856e4d81b6f8 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | wdwvt1/scikit-bio | skbio/stats/distance/tests/test_base.py | Python | bsd-3-clause | 23,628 | [
"scikit-bio"
] | dce83bbc0f242e968015fc212a9bc06fbfeed0150360950bbb31697d1351ee23 |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
#
ANSIB... | alxgu/ansible | lib/ansible/modules/network/avi/avi_webhook.py | Python | gpl-3.0 | 3,916 | [
"VisIt"
] | 228641034df9b3f4a3662013cedfac6e8bb82a0fb5045dc9f1603e53abfbf83a |
# Copyright 1999-2000 by Jeffrey Chang. All rights reserved.
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Record classes to hold BLAST output.
Classes:
Blast Holds all the inform... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/Blast/Record.py | Python | apache-2.0 | 12,546 | [
"BLAST",
"Biopython"
] | 3846547b881bbc27e100555a4ca71872d2c49f8a3f9b9cc4a8d7791d5df7166a |
########################################################################
# $HeadURL$
# File: Operation.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2012/07/24 12:12:05
########################################################################
""" :mod: Operation
===============
.. module: Operation
:... | avedaee/DIRAC | RequestManagementSystem/Client/Operation.py | Python | gpl-3.0 | 13,684 | [
"DIRAC"
] | 500334805d2c7b438e8a57e36c93c631a4f76f736f20e799bc2a13b1f73c0f5d |
"""This demo solves the Stokes equations, using quadratic elements for
the velocity and first degree elements for the pressure (Taylor-Hood
elements). The sub domains for the different boundary conditions
used in this simulation are computed by the demo program in
src/demo/mesh/subdomains."""
# Copyright (C) 2007 Kris... | MiroK/DolfinSurface | demo/undocumented/stokes-taylor-hood/python/demo_stokes-taylor-hood.py | Python | gpl-3.0 | 2,558 | [
"VTK"
] | 2b31fd45e6a744f1c0220fe144a31f93ada7dd56a98070589d2c26c6d3e7946f |
"""Dirac notation for states."""
from sympy import Expr
from sympy.printing.pretty.stringpict import prettyForm
from sympy.physics.quantum.qexpr import (
QExpr, dispatch_method
)
__all__ = [
'KetBase',
'BraBase',
'StateBase',
'State',
'Ket',
'Bra',
'TimeDepState',
'TimeDepBra',
... | GbalsaC/bitnamiP | venv/lib/python2.7/site-packages/sympy/physics/quantum/state.py | Python | agpl-3.0 | 14,797 | [
"DIRAC"
] | d93a72e0634f997e0a36718c7ec6283f335f55c36750abd0dc7ffb8ab6bba1d2 |
#!/usr/bin/env python
# Copyright (c) 2015, Ecole Polytechnique Federale de Lausanne, Blue Brain Project
# All rights reserved.
#
# This file is part of NeuroM <https://github.com/BlueBrain/NeuroM>
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the fol... | juanchopanza/NeuroM | neurom/check/runner.py | Python | bsd-3-clause | 6,308 | [
"NEURON"
] | bdd4ea89933b2f6fbcb29e5f38399b51d24442c5c23a7953855524c3b73e15e1 |
# import_export_maplight/views.py
# Brought to you by We Vote. Be good.
# -*- coding: UTF-8 -*-
from django.contrib import messages
from django.core.urlresolvers import reverse
from django.http import HttpResponseRedirect
from django.shortcuts import redirect
from .controllers import import_maplight_from_json
def imp... | wevoteeducation/WeVoteBase | import_export_maplight/views.py | Python | mit | 828 | [
"VisIt"
] | 634f28ce83f341aa158a8e1469f297e93df5854905c390a376241288b97cdd90 |
#!/usr/bin/env python
#
# Electrum - Lightweight Bitcoin Client
# Copyright (C) 2015 Thomas Voegtlin
#
# 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... | joelstanner/electrum | plugins/trustedcoin/qt.py | Python | gpl-3.0 | 10,743 | [
"VisIt"
] | b45139b60383e0e8098eb6fdb3dbc480766856398c911a33a7fc05581bd3b0e1 |
from igraph import Graph
from pynsett.drt import Drs
class DrsNERCleaner:
def __init__(self, words_without_entity):
self._words_without_entity = words_without_entity
def visit(self, g):
if not isinstance(g, Graph):
raise TypeError("DrsRule.visit_to_graph() needs an igraph.Graph a... | fractalego/pynsett | pynsett/knowledge/drs_ner_cleaner.py | Python | mit | 485 | [
"VisIt"
] | 344eefc689bd78e242e5ef8ffaddd7a34272614f1b87960296e1b0ca11b5dfe5 |
# Copyright 2016 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | tensorflow/tensorflow | tensorflow/python/autograph/converters/logical_expressions.py | Python | apache-2.0 | 4,383 | [
"VisIt"
] | 4a9ef4c0f86a55c8f4d1ece1ca2dab133bc9ecb4154ba2ca73b904ed9a691059 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | pli3/Openwebif | plugin/controllers/views/mobile/channels.py | Python | gpl-2.0 | 6,483 | [
"VisIt"
] | 20108ddacecdddee9b2bfaa316c65e2e2c074e5f1b0ed0ca4a74df693cc319be |
#!/usr/bin/env python3
# Nengo Statistical Inference Implementation for the UWaterloo course SYDE 750
# Copyright (C) 2017 Andreas Stöckel
#
# 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, eith... | astoeckel/syde_750_project_lifespan_inference | code/analyse_net_probability_distribution_err.py | Python | gpl-3.0 | 3,307 | [
"Gaussian"
] | f41d4729f3fafbba3938afc4261abaf49a86512e8d772ceb0ab3c58051cc5bd6 |
# Author: Travis Oliphant, 2002
#
# Further updates and enhancements by many SciPy developers.
#
from __future__ import division, print_function, absolute_import
import math
import warnings
from collections import namedtuple
import numpy as np
from numpy import (isscalar, r_, log, sum, around, unique, asarray,
... | jonycgn/scipy | scipy/stats/morestats.py | Python | bsd-3-clause | 82,932 | [
"Gaussian"
] | 3442af57594ea48f0580ee42925e793ebf929f998a62ac5957aeb29afe59ee31 |
# Run this with:
# python setup.py install --install-lib=.
from __future__ import print_function
from distutils.core import setup, Extension
from rdkit import RDConfig
# force the use of g++ please
from distutils import sysconfig
save_init_posix = sysconfig._init_posix
def my_init_posix():
print('my_init_posix: c... | rvianello/rdkit | Code/Demos/boost/python_objs/setup.py | Python | bsd-3-clause | 1,413 | [
"RDKit"
] | ea4a1ed45cb110ea67b96f216104ecf540589df0280f2f0566c6fea643a411ff |
#!/usr/bin/env python
# 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, software... | appium/python-client | appium/webdriver/extensions/search_context/android.py | Python | apache-2.0 | 9,758 | [
"ESPResSo"
] | 4063757982f51e9741f09dbf236d4ef1ab76006aa4d9569585a1dc5ae35b59dc |
from sys import exit
from random import randint
notebook = []
class Notebook():
def checkBook(self):
if len(notebook) == 0:
print "There is nothing in the notebook"
else:
print notebook
def addbook(self, note):
notebook.append(note)
class Scene(object):
def enter(self):
print "This scene is ... | aleksl05/IS-206 | ex43.py | Python | gpl-3.0 | 8,465 | [
"BLAST"
] | f49fe74b439a8511ce6ef9114773783e17dc82067bcefe21498b2c794a1c512d |
#
# @file TestStoichiometryMath.py
# @brief SBML StoichiometryMath unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Sarah Keating
#
# $Id$
# $HeadURL$
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automa... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/sbml/TestStoichiometryMath.py | Python | gpl-3.0 | 4,795 | [
"VisIt"
] | 536bc691ad3d6de99a57844a6152d23a61fcb1321d69294d033a3b58587e2f60 |
# 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 Pism(CMakePackage):
"""Parallel Ice Sheet Model"""
homepage = "http://pism-docs.org/w... | iulian787/spack | var/spack/repos/builtin/packages/pism/package.py | Python | lgpl-2.1 | 5,975 | [
"NetCDF"
] | a290778d66e538332f02c879399614e3fb21bbd388167489e8ad65a4239367de |
import logging
from netCDF4 import num2date
log = logging.getLogger(__name__)
def get_monthly_time_slices(ncvar_time):
'''
Based on an input NetCDF4 time variable returns calendar appropriate monthly slices
'''
assert 'calendar' in ncvar_time.ncattrs(), "Time variable does not have a defined calendar... | pacificclimate/pyclimate | pyclimate/nchelpers.py | Python | gpl-3.0 | 3,648 | [
"NetCDF"
] | b7714a18a92db785fa6bde9ee2ca019bbc86df2ecbedc7f98e4fe5d8ed896db1 |
import pandas as pd
import os
import ipdb
import numpy
from Bio import SeqIO
import subprocess
from Modules.f00_Message import Message
from natsort import natsorted
import matplotlib.pyplot as plt
import matplotlib as mpl
from multiprocessing import Process
mpl.style.use('ggplot')
import pysam
from Bio.Seq import Seq
... | shl198/Pipeline | nothing.py | Python | mit | 4,880 | [
"HTSeq",
"pysam"
] | aab13d956ed14d4810fa07f01870db0b73fa07794f8494f4eac5211be4d99ea8 |
# -*- coding: utf-8 -*-
import numpy as np
import scipy.special
from bokeh.plotting import *
from bokeh.objects import Range1d
mu, sigma = 0, 0.5 # NOTE: you can tinker with these values if you like
# sample the distribution
measured = np.random.normal(mu, sigma, 10000)
hist, edges = np.histogram(measured, de... | sahat/bokeh | sphinx/source/tutorial/exercises/histogram.py | Python | bsd-3-clause | 3,091 | [
"TINKER"
] | 1923b75611b1d708b406766a0af36d813ac26decb44f8ff5d9b046a7c6fc6a70 |
import pysam
import sys
import os
import pandas as pd
import numpy as np
import glob
import math
class PhasedRatio(object):
def __init__(self, sam_path, bed_path, shs_path, m):
self.sam_path = sam_path
self.bed_path = bed_path
self.shs_path = shs_path
self.m = m
def abund_sRNA(sel... | BleekerLab/Solanum_sRNAs | scripts/Class_PhasedRatio.py | Python | mit | 11,617 | [
"pysam"
] | 75272ae80204667c4eaa035fe6f533fdf46ca422c16f664fe5cf7aaef35c0c3c |
"""!
@brief Oscillatory Neural Network based on Hodgkin-Huxley Neuron Model
@details Implementation based on paper @cite article::nnet::hnn::1.
@authors Andrei Novikov (pyclustering@yandex.ru)
@date 2014-2020
@copyright BSD-3-Clause
"""
from scipy.integrate import odeint
from pyclustering.core.wrapper... | annoviko/pyclustering | pyclustering/nnet/hhn.py | Python | gpl-3.0 | 26,232 | [
"NEURON",
"exciting"
] | b629b0ab4a4bea58dd6d68a9392786ff026e0523dc30eb3cced91a3607541163 |
import theano
import theano.tensor as TT
import numpy as np
from simple_lenet import LeNetClassifier
import layers
class AlexNet(LeNetClassifier):
""" Special class specifically for Alexnets. It handles the initialization and
special testing methods. """
def __init__(self, train, test, batch_size, layer_over... | djpetti/rpinets | theano/alexnet.py | Python | mit | 7,830 | [
"Gaussian"
] | e22798962e62ca8cc9e378d017e67989b4c1188025d832a59cef6a4bb84cf73a |
# -*- 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/coordinates/FHIAIMS.py | Python | gpl-2.0 | 11,259 | [
"FHI-aims",
"MDAnalysis"
] | 967f710c80bd6e9898202b33f9ef62f3f566f304e61c5c23031da3134726ad99 |
# pysam versioning information
__version__ = "0.4.2"
__samtools_version__ = "0.1.13"
__tabix_version__ = "0.2.3"
| mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/eggs/pysam-0.4.2_kanwei_b10f6e722e9a-py2.7-linux-x86_64-ucs4.egg/pysam/version.py | Python | gpl-3.0 | 116 | [
"pysam"
] | e33dea0e9759fe04aa42f27e463c87b6c4f0ea3a9ddf8c490e9b0bc81ceaee0d |
#!/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... | bjolivot/ansible | lib/ansible/modules/network/avi/avi_networkprofile.py | Python | gpl-3.0 | 3,721 | [
"VisIt"
] | 7bf61b477b13057bc648471f1619cbdaf2452cc6cfcb1fdc5ebb1fc764b10083 |
from pysam import CINS, CSOFT_CLIP, CHARD_CLIP
from dark.sam import CONSUMES_REFERENCE
# From https://samtools.github.io/hts-specs/SAMv1.pdf
(CINS_STR, CDEL_STR, CMATCH_STR, CEQUAL_STR, CDIFF_STR,
CHARD_CLIP_STR) = 'IDM=XH'
def dna2cigar(s1, s2, concise=False):
"""
Form a CIGAR string from two equal-lengt... | acorg/dark-matter | dark/cigar.py | Python | mit | 9,894 | [
"pysam"
] | d7a90f40672c7878e85d1a3d57e10e55853078bef8a14745da1e4e9a0dd682c6 |
# .. coding: utf8
# $Id: __init__.py 7078 2011-07-07 07:06:41Z grubert $
# Author: Engelbert Gruber <grubert@users.sourceforge.net>
# Copyright: This module has been placed in the public domain.
"""LaTeX2e document tree Writer."""
__docformat__ = 'reStructuredText'
# code contributions from several people included, ... | paaschpa/badcomputering | docutils/writers/latex2e/__init__.py | Python | bsd-3-clause | 120,484 | [
"VisIt"
] | 44c6b82e68af83e1af61ef8c7b1b84fa6d45b2b613d2d197879b9e2ceb64bd25 |
#
# Copyright (C) 2013-2018 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... | mkuron/espresso | testsuite/python/layered.py | Python | gpl-3.0 | 1,832 | [
"ESPResSo"
] | 1d49dfcbd94e0e7afd2797b52963ab4ef8d5a8daf9dda4f525f3d0093884eac6 |
#!/usr/bin/env python3
#pylint: disable=missing-docstring
#* 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
... | nuclear-wizard/moose | python/chigger/tests/graphs/dualx.py | Python | lgpl-2.1 | 910 | [
"MOOSE"
] | a0d25477f5558d37b7f4cc10d2ac2e0b6d5171fd3c777c10a5edb8f5084a3ada |
#pylint: disable=missing-docstring
#* 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/... | nuclear-wizard/moose | python/chigger/RenderWindow.py | Python | lgpl-2.1 | 12,198 | [
"MOOSE",
"VTK"
] | ccd5618f9f03cc2ca30ff33ded2c1cb07d6823ba5ff220bf4d1610b97a284040 |
#!/usr/bin/env python
import sys
import numpy as np
import pychemia
from pychemia.visual.searcher import *
from matplotlib.backends.backend_pdf import PdfPages
import matplotlib.pyplot as plt
from pychemia.crystal import CrystalSymmetry
import matplotlib.lines as mlines
import matplotlib.patches as mpatches
from matpl... | MaterialsDiscovery/PyChemia | scripts/Report_Orbital.py | Python | mit | 18,575 | [
"CRYSTAL",
"Firefly"
] | 8145ddf5db82115e93ec465fc0d5d31ace168d0fd3a39d68b76e7c91c098bee4 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
import unittest
import os
import random
import json
import numpy as np
from ruamel.yaml import YAML
from pymatgen impor... | setten/pymatgen | pymatgen/io/lammps/tests/test_data.py | Python | mit | 26,308 | [
"LAMMPS",
"pymatgen"
] | e4658424302c88b4e89adda3d87a0ba68524b6ec969d0d5a3dca3d40643cf81a |
## Chose what kind of fit to perform.
fit_kind="ESP+TDF"
#fit_kind="ESP"
#fit_kind="RESP"
#fit_kind="RG"
#coor="zif8.pdb"
coor="zif8.xyz"
## ESP control section
esp_from_cp2k=True
## first gamma value
g_start=0.6
## increase step
g_step=0.1
## number of gammas
n_gammas=20
## TDF control section (for ESP only fit th... | cpctools/infinicharges | examples/sample_InfiniInput.py | Python | gpl-3.0 | 1,378 | [
"CP2K"
] | 10637f6ce3128393bb6e7266ef292713c3798f81e6de6679e215f805f19d6ad3 |
#! /usr/bin/env python
"""Module to create diagnostic PNGs for checking ramps in a visit or
subset of visits.
*Step 2 of Prep.*
Checks:
Flip through the PNGs. If bad reads found, you will need to mark them
to be popped in :mod:`reprocess_all.py`.
For earth-flat persistence, or any anamoly that affect... | ivastar/clear | check_all.py | Python | mit | 3,911 | [
"VisIt"
] | e640190f37ef7d2fd47e232438b9fdf72b4813ed30c3f1ef3f992df4bbf3a7be |
#!/usr/bin/env python
import glob
import sys
from subprocess import call
from collections import Counter
import multiprocessing
import time
start_time = time.time()
'''
Author: Marion Shadbolt
Email: marion.shadbolt@gmail.com
Last updated: 28/10/2016
Program Description:
Script to align pre-processed reads to male... | mshadbolt/Ae_aegypti-toolset | ThesisScripts/Python/MaleDiagnosis/MaleDiag.py | Python | mit | 11,313 | [
"Bowtie"
] | 5adca7429a1d57f99516c5a86a39a1d036316ec76c33fe47b48efb7800227e0d |
# -----------------------------------------------------------------------------
#
# Copyright (C) 2021 CERN & University of Surrey for the benefit of the
# BioDynaMo collaboration. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance w... | BioDynaMo/biodynamo | test/unit/core/visualization/paraview/validate_agents.py | Python | apache-2.0 | 3,553 | [
"ParaView"
] | 0db7374a2d93949d47206e1f78cd85c5e4249492c6884e7f75875268d2b38ebc |
""" Module for QA plots
"""
from __future__ import print_function, absolute_import, division
import os
import numpy as np
from scipy import signal
import scipy
import scipy.stats
import pdb
import copy
from astropy.time import Time
from desiutil.log import get_logger
from desispec import fluxcalibration as dsflux
fr... | desihub/desispec | py/desispec/qa/qa_plots.py | Python | bsd-3-clause | 51,575 | [
"Gaussian"
] | 39cfce1f16a03689e7ad67588293beda1820615d7c9671d9537008acabdc1850 |
# Copyright (c) 2018, Alejandro Molina-Sanchez
# All rights reserved.
#
# This file is part of the yambopy project
#
from yambopy import *
from yambopy.plot import *
import os
class YamboRTMovie(YamboSaveDB):
"""
Create a file with data of real time simulations performed with Yambo
"""
def __init__(se... | alexmoratalla/yambopy | yambopy/rt/rt_movie.py | Python | bsd-3-clause | 9,918 | [
"Yambo"
] | 4dfa7f3034f9fea1bbc07b5bf1f004f7c1fd5ae8c6b5baac399620e50adebbb6 |
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
#
"""
This is an implementation of a state-emitting MarkovModel. I am using
terminology similar to Manning and Schutze.
Functions:
train_bw T... | zjuchenyuan/BioWeb | Lib/Bio/MarkovModel.py | Python | mit | 22,686 | [
"Biopython"
] | bcedebb6194d5d6f7180eba3ca2e75eaf2ca8e320a47be3797581c6a0f99904d |
"""
Functions to transform / filter sequences
"""
import collections
import contextlib
import copy
import cPickle as pickle
import gzip
import itertools
import logging
import re
import string
import tempfile
import random
from Bio import SeqIO
from Bio.Alphabet import IUPAC
from Bio.Data import CodonTable
from Bio.Seq... | smilefreak/ancient_dna_pipeline | src/seqmagick/seqmagick/transform.py | Python | mit | 25,874 | [
"Biopython"
] | 63bdd1512be0f6b10bee547915a4d6f5d591660c7e1e069ac8dcb04fd662007e |
#
# Copyright (C) 2013-2019 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... | fweik/espresso | testsuite/python/wang_landau_stats.py | Python | gpl-3.0 | 4,857 | [
"ESPResSo"
] | ad86b4df78377a79e48208d32517104dd061f9f11916e9d48e18dd45af96dea6 |
import datetime
import re
from django.contrib.auth.models import (
AbstractBaseUser,
BaseUserManager,
PermissionsMixin,
)
from django.core.exceptions import ValidationError
from django.core.validators import MinValueValidator, RegexValidator
from django.db import models, transaction
from django.db.models i... | swcarpentry/amy | amy/workshops/models.py | Python | mit | 96,111 | [
"VisIt"
] | 4cee544ed05d121a37aebe22c97c59a7ae888f0b9809705da8c0842d92b6f219 |
#!/usr/bin/env python
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
'''The 'grit menufromparts' tool.'''
import types
from grit import grd_reader
from grit import tclib
from grit import util
from g... | guorendong/iridium-browser-ubuntu | tools/grit/grit/tool/menu_from_parts.py | Python | bsd-3-clause | 2,581 | [
"xTB"
] | cf651ddc8f97e57db7a3c2138d0983427ca676841ebbaa30e375d5307174c6c7 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
from monty.os.path import which
from monty.serialization import dumpfn, loadfn
from pymatgen.core.structure import Molecule
from pymatgen.io.qchem.outputs import QCOutput, check_for... | davidwaroquiers/pymatgen | pymatgen/io/qchem/tests/test_outputs.py | Python | mit | 8,421 | [
"pymatgen"
] | 27da366c698d93e36ec6ea80688a34bbe4ffebf533a049fe1cac14599a0368ee |
# -*- coding: utf-8 -*-
"""
moe.wiki.model
~~~~~~~~~~~~~~
Models for wiki pages and revisions.
:copyright: 2009 by tipfy.org.
:license: BSD, see LICENSE.txt for more details.
"""
import datetime
from google.appengine.ext import db
from tipfy.ext.wtforms import Form, fields, validators
from tipf... | ac001/moe | project/app/moe/wiki/models.py | Python | bsd-3-clause | 8,911 | [
"MOE"
] | 62e332e6959c149a933d56a96a05854af2f2941b20de75f2f010534294566aea |
#!/usr/bin/env python
import argparse
import json
import os
import re
from maec.package import Package
from maec.package import MalwareSubject
from stix.core import STIXPackage, STIXHeader
from stix.common.information_source import InformationSource
from stix.indicator.indicator import Indicator
from cybox.core impor... | utkonos/malcrawler | har2stix.py | Python | apache-2.0 | 4,959 | [
"VisIt"
] | b02e465774c3fec99e0ef2265a9bc2df0a8fa05bb1a597e3dbc5baffe7f2fe64 |
from __future__ import absolute_import
import unittest
import math
import numpy as np
from pymatgen.analysis.elasticity.tensors import SQTensor
from pymatgen.util.testing import PymatgenTest
class SQTensorTest(PymatgenTest):
def setUp(self):
self.rand_sqtensor = SQTensor(np.random.randn(3, 3))
... | migueldiascosta/pymatgen | pymatgen/analysis/elasticity/tests/test_tensors.py | Python | mit | 5,912 | [
"pymatgen"
] | aca46b8111b59248eaa25b934a1e5da71c7036332bfa4c81c3de8149ae12a244 |
from website import settings
settings.ELASTIC_INDEX = 'test'
import unittest
from nose.tools import * # PEP8 asserts
from tests.base import OsfTestCase
from tests.test_features import requires_search
from tests.factories import (
UserFactory, ProjectFactory, NodeFactory,
UnregUserFactory, UnconfirmedUserFact... | kushG/osf.io | tests/test_elastic.py | Python | apache-2.0 | 17,573 | [
"Brian"
] | a5ee6491dc97f834b05658eaa909857f0ba86a11a9198c67d9801e7deada5d91 |
from __future__ import division, print_function, absolute_import
__all__ = ['fixed_quad','quadrature','romberg','trapz','simps','romb',
'cumtrapz','newton_cotes']
from scipy.special.orthogonal import p_roots
from scipy.special import gammaln
from numpy import sum, ones, add, diff, isinf, isscalar, \
a... | chaluemwut/fbserver | venv/lib/python2.7/site-packages/scipy/integrate/quadrature.py | Python | apache-2.0 | 27,827 | [
"Gaussian"
] | f8abd45c4716a8962c8cbc1d913b816435dd194afd04748d6af7f47ad4fff63a |
from Bio.Blast import NCBIWWW
fasta_string = open("sequence.fa").read()
result_handle = NCBIWWW.qblast("blastn", "nt", fasta_string)
from Bio.Blast import NCBIXML
blast_record = NCBIXML.read(result_handle)
for alignment in blast_record.alignments:
for hsp in alignment.hsps:
if hsp.expect >= 0.00000000000005: conti... | m1key/genomic-data-science | run.py | Python | mit | 585 | [
"BLAST"
] | f07603276fc48ce73e632579d550eabc0c41fae120fff984077e9205f728f578 |
from __main__ import vtk, qt, ctk, slicer
class SkinModelMakerLogic:
def __init__(self):
# VTK Signals variables
self.Observations = []
self.StatusModifiedEvent = slicer.vtkMRMLCommandLineModuleNode().StatusModifiedEvent
# Parameters dictionnaries
self.ChangeLabelParameters = {}
self.Generat... | ricortiz/BenderCraniosynostosis | Modules/Scripted/SkinModelMaker/SkinModelMaker.py | Python | apache-2.0 | 13,701 | [
"VTK"
] | a77c206e840ad6e48781f253a10df31bc8a4ce40bed17ae337b8473c1423a958 |
# ========================== Start Copyright Notice ========================== #
# #
# Copyright 2014 F.D.I.S. #
# This file is part of Kinetic Gunner: Gunner of Angst ... | CertainlyUncertain/Kinetic-Gunner-Gunner-of-Angst | sndMgr.py | Python | gpl-3.0 | 4,016 | [
"VisIt"
] | fdb2e4bb5f7c157fd166312610095493af7671efc4f11deb96bd60ffbaf2a370 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module provides classes that operate on points or vectors in 3D space.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2011, The Materi... | sonium0/pymatgen | pymatgen/core/operations.py | Python | mit | 15,024 | [
"pymatgen"
] | 3b814c51cd8e9a69467ba48f836308084cd7136a0660df3fe1a3d4793d164a56 |
""" Simple multi-layer perception neural network using Minpy """
# import minpy
import minpy.numpy as np
from minpy.nn import layers
from minpy.nn.model import ModelBase
from minpy.nn.solver import Solver
from minpy.nn.io import NDArrayIter
from examples.utils.data_utils import get_CIFAR10_data
from minpy.context impor... | shadowleaves/deep_learning | twolayer/minpy_only.py | Python | mit | 3,068 | [
"Gaussian"
] | f224cadd0a2db1cfd8f0ed27ecbddcd36e5574fed1121e241046f89d130e104d |
#!/usr/bin/env python
import os
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Read a field representing unstructured grid and display it (similar to blow.tcl)
# create a reader and write out field data
reader = vtk.vtkUnstructuredGridReader()
reade... | ashray/VTK-EVM | Filters/Core/Testing/Python/fieldToUGrid.py | Python | bsd-3-clause | 4,378 | [
"VTK"
] | 411d36b5487d5b6f547cd34cbcad15186b6aa5a86a2f4aa7f7250ccd4b6eaa6a |
import time
import numpy
from simphony.core.cuba import CUBA
from simphony.core.keywords import KEYWORDS
from ..common.atom_style_description import ATOM_STYLE_DESCRIPTIONS
from ..common.atom_style import get_lammps_string
class LammpsDataFileWriter(object):
""" Class writes Lammps data file
Lammps data ... | simphony/simphony-lammps-md | simlammps/io/lammps_data_file_writer.py | Python | bsd-2-clause | 5,724 | [
"LAMMPS"
] | a85064035a227c3a09a751d26ce9541e98c73505bd0884752036b360584516a9 |
#!/usr/bin/env python
from pylab import *
import os
from scipy.stats.stats import spearmanr
from scipy.stats import ks_2samp
from scipy.stats import scoreatpercentile
from scipy.stats.mstats import normaltest
from anderson import *
pscale24=2.45#arcsec per pixel
pscalesdss=1.#arcsec per pixel
sdsspixelscale=0.396127#... | rfinn/LCS | python/LCScommon.py | Python | gpl-3.0 | 21,030 | [
"Galaxy"
] | efddce9a83089796370f2d75619c0e6f1c6a092a67bda67cd756e2e38e162649 |
"""Copy number detection using read counts, with cn.mops.
http://www.bioconductor.org/packages/release/bioc/html/cn.mops.html
"""
from contextlib import closing
import os
import re
import shutil
import subprocess
import pysam
import toolz as tz
from bcbio import bam, install, utils
from bcbio.distributed.multi impor... | Cyberbio-Lab/bcbio-nextgen | bcbio/structural/cn_mops.py | Python | mit | 11,153 | [
"Bioconductor",
"pysam"
] | 1bc3e467e25758ae4590512be23aa8d750c5e3043bff0acb47c557873aff831d |
#!/usr/bin/env python
import vtk
# create a rendering window and renderer
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
renWin.SetSize(300,300)
# create an actor and give it cone geometry
cone = vtk.vtkConeSource()
cone.SetResolution(8)
coneMapper = vtk.vtkPolyDataMapper()
coneMapper... | naucoin/VTKSlicerWidgets | Graphics/Testing/Python/cameraWarpedCone.py | Python | bsd-3-clause | 1,048 | [
"VTK"
] | b389e4a36a2a033193d23c0988216becc49fc8faf70f4f76bc1d1b5ff661ec1a |
"""
Module to test the one-dimensional plotting of NetCDF files
More tests can be found in the manual_integration_tests package
"""
import unittest
import iris
from iris.coords import DimCoord
from iris.cube import Cube
import numpy as np
from cis.data_io.gridded_data import make_from_cube
from cis.plotting.formatted... | cedadev/cis | cis/test/unit/test_plot.py | Python | lgpl-3.0 | 7,751 | [
"NetCDF"
] | e6e2d8e4c3dd0d905a2e82ace5f19d61286d18c5ba34e0c768923f2e31e73a33 |
# coding: utf-8
"""
Vericred API
Vericred's API allows you to search for Health Plans that a specific doctor
accepts.
## Getting Started
Visit our [Developer Portal](https://developers.vericred.com) to
create an account.
Once you have created an account, you can create one Application for
Production and an... | vericred/vericred-python | vericred_client/models/request_provider_notification_subscription.py | Python | apache-2.0 | 13,905 | [
"VisIt"
] | 202da8c09546aec7a2b2148822248be53e33ebf453488de1d8745130687692c2 |
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