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# Package imports
from ..reconstruction.Gaussian_Model import Gaussian_Model
from ..settings.Arguments import Arguments
from reconstruction_model import ModelTestCase
class TestReconstructionGaussianModel(ModelTestCase):
def setUp(self):
super(TestReconstructionGaussianModel, self).setUp()
self.ar... | timvandermeij/mobile-radio-tomography | tests/reconstruction_gaussian_model.py | Python | gpl-3.0 | 2,018 | [
"Gaussian"
] | 9a96363d655288b260100ee4f24e932baca59ba85d1c47c4885aa80156c35a2d |
#!/usr/bin/env python
# Script using Biopython objects to import and adapt PDB files
from Bio.PDB import *
import numpy as np
import requests
import argparse
parser=PDBParser(QUIET=True)
#Protocol
# 1) Read in arguments for downloading PDB files
# 2) Read in table of PDB entries and CDR ranges
# 3) Delete atoms in CD... | rtb1c13/scripts | SAXS_MD/delete_CDR.py | Python | gpl-2.0 | 6,664 | [
"Biopython"
] | 0d6bd6ab894589aa3b7f01bdc58cf9f05cf7a66ed46df5d5f71f8c664af5e998 |
"""Color transfer function related code.
"""
# Author: Prabhu Ramachandran <prabhu@aero.iitb.ac.in>
# Copyright (c) 2006-2009, Enthought, Inc.
# License: BSD Style.
# Enthought library imports.
from traits.api import List
from tvtk.api import tvtk
####################################################################... | liulion/mayavi | tvtk/util/ctf.py | Python | bsd-3-clause | 9,871 | [
"VTK"
] | 900c19d1a5f13afc667400fb058b7d9b061572e03abff28d70d48fad6d502d0e |
#!/usr/bin/env python
#
# This code is part of the binding affinity prediction tools distribution
# and governed by its license. Please see the LICENSE file that should
# have been included as part of this package.
#
"""
Binding affinity predictor based on Intermolecular Contacts (ICs).
Anna Vangone and Alexandre M.... | JoaoRodrigues/binding_affinity | predict_IC.py | Python | apache-2.0 | 7,504 | [
"Biopython"
] | a186550307d2e48e0d2597bb040502e9ce5526633dfb10df4cdc5b8bc6913727 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/e2openplugin-OpenWebif | plugin/controllers/views/web/signal.py | Python | gpl-2.0 | 5,514 | [
"VisIt"
] | 2fe8996302dd0a8cfcc543b989c239bef4ea9599e02298d27613dea041de05a8 |
import galaxy_analysis as ga
import glob
import os
import numpy as np
import sys
import re
from galaxy_analysis.misc import process_boundary_flux as pbf
from joblib import Parallel, delayed
import multiprocessing
import yt
yt.funcs.mylog.setLevel(40)
def _parallel_loop(i):
if not os.path.isfile('DD%0004i/DD%0... | aemerick/galaxy_analysis | examples/compute_everything.py | Python | mit | 1,965 | [
"Galaxy"
] | a79350fd20e33d701ad738b4984cbea5bae3fa1735049ba1b1aaa2d526d4aaa9 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
from math import pi, sqrt, log
from datetime import datetime
from copy import deepcopy, copy
from warnings import warn
import bisect
import numpy as np
from s... | matk86/pymatgen | pymatgen/analysis/ewald.py | Python | mit | 24,382 | [
"GULP",
"pymatgen"
] | 92c60fa2e40f70939df5a8adb73a0dcf4d451d2f8a7e7877d3b07ae85816b9aa |
#!/usr/bin/python
import httplib
import httplib2
import os
import random
import sys
import time
from googleapiclient.discovery import build
from googleapiclient.errors import HttpError
from googleapiclient.http import MediaFileUpload
from oauth2client.client import flow_from_clientsecrets
from oauth2client.file impor... | sandeepraju/git-talk | gittalk/upload_youtube.py | Python | bsd-3-clause | 8,485 | [
"VisIt"
] | eaef5c2b6ca4cb9e6374861fe2eae1f63f44a4bc62e3a16512aaf944b5edf432 |
# plugin: helixbundle.py
# Copyright (c) 2010 Oliver Beckstein <orbeckst@gmail.com>
# Released under the GNU Public License 3 (or higher, your choice)
# See the file COPYING for details.
"""
Helix bundle analysis
=====================
Analysis of helix bundles with :func:`gromacs.g_bundle`.
.. SeeAlso:: HELANAL does... | jandom/GromacsWrapper | gromacs/analysis/plugins/helixbundle.py | Python | gpl-3.0 | 12,492 | [
"Gromacs"
] | e732e08520991d87e58fbd8e4422dc29440ba5b6def7504948fa60efa4fdd972 |
import ocl as cam
import camvtk
import time
import vtk
import math
import datetime
def drawellipse(myscreen, ellcenter, a_axis, b_axis):
resolution=50
for n in xrange(0,resolution):
angle1= (float(n)/float(resolution))*2*math.pi
angle2= (float(n+1)/float(resolution))*2*math.pi
x=ellcent... | JohnyEngine/CNC | opencamlib/scripts/offset-ellipse/oellipse4_tst.py | Python | apache-2.0 | 7,423 | [
"VTK"
] | 35438526e7a40dc320dc2a585d7c56ba86fa102222a8e8fbd9239f6883cb0dec |
# Copyright (c) 2012, GPy authors (see AUTHORS.txt).
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import numpy as np
from ...util.linalg import pdinv, dpotrs, dpotri, symmetrify, jitchol
class Posterior(object):
"""
An object to represent a Gaussian posterior over latent function values, p(f|D)... | ptonner/GPy | GPy/inference/latent_function_inference/posterior.py | Python | bsd-3-clause | 6,888 | [
"Gaussian"
] | 0e3b6082fe9d4d6f2274d758c46ce0e10a7cbf255e0e4bec1bb55f22a00d693b |
# coding: utf-8
from __future__ import unicode_literals
import unittest
import os
from pymatgen.analysis.ewald import EwaldSummation, EwaldMinimizer
from pymatgen.io.vasp.inputs import Poscar
import numpy as np
test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..",
'test_files'... | rousseab/pymatgen | pymatgen/analysis/tests/test_ewald.py | Python | mit | 4,262 | [
"VASP",
"pymatgen"
] | f27f4caf16599bf1356825bf0964ae2fb275f10d4481011741c1218a014ffbd7 |
#!/usr/bin/env python3
from LoLIM.interferometry.interferometry_absBefore import interferometric_locator
## these lines are anachronistic and should be fixed at some point
from LoLIM import utilities
utilities.default_raw_data_loc = "/exp_app2/appexp1/public/raw_data"
utilities.default_processed_data_loc = "/home/br... | Bhare8972/LOFAR-LIM | LIM_scripts/interferometry/examples/run_3Dinterferometry_absBefore.py | Python | mit | 2,688 | [
"Brian"
] | 0ea70c2fa9ee7d9c9625168bc4ec86fbdd7636a48f1551c5609a3ce0673c43e2 |
import random, copy
from multiprocessing import Pool
import test
from pybrain.structure import RecurrentNetwork
from pybrain.structure import FeedForwardNetwork
from pybrain.structure import LinearLayer, SigmoidLayer
from pybrain.structure import FullConnection
from sklearn import svm
import numpy as np
import scipy.sp... | divir94/News-Analytics | evolutionaryNN.py | Python | apache-2.0 | 6,232 | [
"NEURON"
] | ba939018ac34b9ff2ebb59d5074c32eec23ef370fae311ab66837904746d0a0e |
Info="""
Module name: lmp2xyz.py
Author: (c) Andres Jaramillo-Botero
California Institute of Technology
ajaramil@caltech.edu
Project: pEFF
Version: August 2009
Extracts the xyz from a lammps trajectory dump of style custom:
dump 1 all custom period dump_file id type x y z spin radius ...
Usage: python lmp2xyz.py... | browndeer/lammps-ocl | tools/eff/lmp2xyz.py | Python | gpl-2.0 | 3,539 | [
"LAMMPS"
] | 63ae0c4857ca5796803e8726b3975571c1f60db86cd611491175855e050e5b44 |
# Copyright 2019 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... | cxxgtxy/tensorflow | tensorflow/python/keras/layers/preprocessing/image_preprocessing.py | Python | apache-2.0 | 54,989 | [
"Gaussian"
] | 90e053a2880598a0445551a398071715790cdf84b3af9d41662f21b08585f000 |
__all__ = ["ui", "oi", "utilities"]
bl_info = {
"name": "Export Crystal Space 3D format",
"description": "Export meshes, scenes and animations",
"author": "The Crystal Space team",
"version": (2, 1),
"blender": (2, 5, 9),
"api": 39685,
"location": "The main panel is in 'Properties > Render'... | baoboa/Crystal-Space | scripts/blender/io_scene_cs/__init__.py | Python | lgpl-2.1 | 1,389 | [
"CRYSTAL"
] | 7a80251594033ca65c02e1104cebd8f9d8ac41358dabe5e57d68590e69b1d293 |
# coding: utf-8
# # Diffusion computation
# https://github.com/alvason/diffusion-computation
#
# ### Lecture003 --- Stochastic solution for the diffusion equation
# In[1]:
'''
author: Alvason Zhenhua Li
date: 03/19/2015
'''
get_ipython().magic(u'matplotlib inline')
import numpy as np
import matplotlib.pyplot a... | alvason/diffusion-computation | stochasticD/diffusion_stochastic.py | Python | gpl-2.0 | 4,267 | [
"Gaussian"
] | 08edd1186eacc3bf5803251814e87c25a7c64e95fabec4371d82d64472ab3fee |
"""Unit tests
"""
import app
import unittest
class CrossUploadPage(unittest.TestCase):
"""Tests the upload page functionality
"""
def setUp(self):
"""Set up variables
"""
app.APP.config["TESTING"] = True
self.app = app.APP.test_client()
def tearDown(self):
""" Tear down variables
"""
... | ColCarroll/cross_tracker | tests.py | Python | mit | 483 | [
"VisIt"
] | f5ad8dae1bcd2877cf02e42036f39b365006b3f1ebae7903bf83da4e1205a6dc |
import unittest
from models import heliosat
import numpy as np
from netcdf import netcdf as nc
from datetime import datetime
import os
import glob
class TestPerformance(unittest.TestCase):
def setUp(self):
# os.system('rm -rf static.nc temporal_cache products')
os.system('rm -rf temporal_cache pr... | ahMarrone/solar_radiation_model | tests/performance_test.py | Python | mit | 1,278 | [
"NetCDF"
] | 0136f2b36ab1a58ee6bf6fa89ef063ce8a86488f415abc8dbbaabf88e04f78bc |
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by appl... | gkc1000/pyscf | pyscf/nao/m_ao_eval_libnao.py | Python | apache-2.0 | 3,652 | [
"PySCF"
] | f52b2d4510f3d886a9b5a7fe00c9b006a2595a1864003a9432ef7f2130d98510 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
#
# Copyright (C) 2020 Stoq Tecnologia <http://www.stoq.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 Software Foundation;... | stoq/stoq-server | stoqserver/api/resources/sellable.py | Python | gpl-2.0 | 7,723 | [
"VisIt"
] | 99d0a4a1ce25653eae32c9bad794f61b04f1a0e5ffca71a3edbd94f70e80f40e |
# -*- coding: utf-8 -*-
# Generated from the Telepathy spec
""" Copyright (C) 2007 Collabora Limited
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or ... | davidedmundson/telepathy-hangups | telepathy/_generated/Connection_Interface_Mail_Notification.py | Python | lgpl-2.1 | 7,367 | [
"VisIt"
] | fd30419f5fe4902d534117d257293fb81a352bef6e3d9fe99d8825c820a1db3d |
# -*- coding: utf-8 -*-
import numpy as np
import abel
import matplotlib.pyplot as plt
IM = np.loadtxt("data/VMI_art1.txt.bz2")
legendre_orders = [0, 2, 4] # Legendre polynomial orders
proj_angles = np.arange(0, np.pi/2, np.pi/10) # projection angles in 10 degree steps
radial_step = 1 # pixel grid
smoothing = 1 #... | DhrubajyotiDas/PyAbel | examples/example_linbasex_hansenlaw.py | Python | mit | 3,148 | [
"Gaussian"
] | 08d6b7f0cb9b8242ea05888ec5e27b3257bff790a8f23b1e63f3c51c72f71854 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# =============================================================================
## @file ostap/fitting/modifiers.py
# Set of useful utilities to modify the certain PDF
# @author Vanya BELYAEV Ivan.Belyaeve@itep.ru
# @date 2018-11-29
# ===================================... | OstapHEP/ostap | ostap/fitting/modifiers.py | Python | bsd-3-clause | 18,145 | [
"Gaussian"
] | fc4db536a1d8611b5a01277b459b41c26878dcf8738672852effd934a3b150c6 |
"""Test functions for linalg._solve_toeplitz module
"""
from __future__ import division, print_function, absolute_import
import numpy as np
from numpy.testing import (run_module_suite, assert_equal, assert_allclose,
assert_raises)
from numpy.testing.decorators import knownfailureif
from scip... | DailyActie/Surrogate-Model | 01-codes/scipy-master/scipy/linalg/tests/test_solve_toeplitz.py | Python | mit | 3,994 | [
"Gaussian"
] | ddef5f11a06885206f90d49d7a9fef4cb7f72eed3f43afbf7c164ddf89fcf559 |
import os
import tempfile
import sys
import pymbar
import numpy as np
import pandas as pd
import simtk.openmm.app as app
import simtk.openmm as mm
import simtk.unit as u
import mdtraj as md
import repex
ff = app.ForceField("tip3p.xml")
def build_top(box_edge=2.1 * u.nanometers, nonbondedMethod=app.CutoffPeriodic):
... | kyleabeauchamp/DBayes | dbayes/water_lib.py | Python | gpl-2.0 | 4,943 | [
"MDTraj",
"OpenMM"
] | e7d231a12cdd6668b9a5dfed1dece0a6096003f360c6b4da6a6d3306b947fef1 |
import sys
import os.path
#sys.path.insert(0, '/home/andy/theano/tool_examples/theano-lstm-0.0.15')
from theano_lstm import Embedding, LSTM, RNN, StackedCells, Layer, create_optimization_updates, masked_loss
from utilities import *
import dill
import argparse
#import cPickle
import pickle
import numpy
from collections... | darongliu/Lstm_Turing_LM | lstm-neural-turing-machines-lm/analysis/v1-one-weight-get-weight/lm_v4.py | Python | mit | 25,087 | [
"NEURON"
] | 86b0209c186d60e2d3e694245609d7c9ecd150dd93c5dedfa887787900927bfc |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The fsl module provides classes for interfacing with the `FSL
<http://www.fmrib.ox.ac.uk/fsl/index.html>`_ command line tools. This
was written to work with FSL version 4.1.4.
Examples
--------
See the... | gerddie/nipype | nipype/interfaces/fsl/utils.py | Python | bsd-3-clause | 81,102 | [
"VTK"
] | f8ea1d7bd7d16a22d894396a9ce68943679fa37cd00c3bb6b1a9c83d80c0a990 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module provides classes and methods used to describe deformations and
strains, including applying those deformations to structure objects and
generating deformed structure sets for further calculation... | gmatteo/pymatgen | pymatgen/analysis/elasticity/strain.py | Python | mit | 8,751 | [
"pymatgen"
] | 81d31e52c312eb309c9e986609ea165f1ef862752fe7144cde16fa362ffc17cd |
"""
=======
Plotter
=======
.. moduleauthor:: Adam Ginsburg <adam.g.ginsburg@gmail.com>
"""
from __future__ import print_function
import matplotlib
import matplotlib.figure
import numpy as np
import astropy.units as u
import copy
import inspect
from astropy import log
# this mess is to handle a nested hell of differe... | e-koch/pyspeckit | pyspeckit/spectrum/plotters.py | Python | mit | 35,855 | [
"Gaussian"
] | eeadd54c7f40528c31aa85a0d1d23b889b84b5dc8efc17584707abcd24d54b24 |
#!/usr/bin/env python
"""Example which shows with the MNIST dataset how Lasagne can be used."""
from __future__ import print_function
import gzip
import itertools
import pickle
import os
import sys
import numpy as np
import lasagne
import theano
import theano.tensor as T
from scipy.linalg import hadamard
from scipy.... | kafluette/ffnnet | ffnnet.py | Python | apache-2.0 | 10,067 | [
"Gaussian"
] | 1fe7963e18fc38269e272cda75fb5fb15ac9bc1a8f70442c57c45c170825ae37 |
from chain.core.api import Resource, ResourceField, CollectionField, \
MetadataCollectionField
from chain.core.api import full_reverse, render_error
from chain.core.api import CHAIN_CURIES
from chain.core.api import BadRequestException, HTTP_STATUS_BAD_REQUEST
from chain.core.api import register_resource
from chain... | ResEnv/chain-api | chain/core/resources.py | Python | mit | 40,049 | [
"VisIt"
] | 4c8e41ee1170851beaf94b9e437aa9fd185e0fd4a297c24a763af860174faa22 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# mingus - Music theory Python package, instrument module.
# Copyright (C) 2008-2009, Bart Spaans
#
# 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 ... | marianinn/mingus | mingus/containers/instrument.py | Python | gpl-3.0 | 6,856 | [
"CRYSTAL"
] | 5a63f8dc3ec41bc1ec9db734a703c966239de55ffcfe25ddefba5c52277a290a |
"""
This is a python reimplementation of the open source tracker in
High-Speed Tracking with Kernelized Correlation Filters
Joao F. Henriques, Rui Caseiro, Pedro Martins, and Jorge Batista, tPAMI 2015
modified by Di Wu
"""
import numpy as np
import matplotlib.pyplot as plt
from scipy.misc import imresize
from skimage.t... | stevenwudi/Kernelized_Correlation_Filter | KCFpy_saliency.py | Python | gpl-3.0 | 63,214 | [
"Gaussian"
] | cd9174fb9909ff0448a3199811537b0301c98733280b7f1803914798c092bee6 |
#!/usr/bin/env python
from __future__ import print_function
import os
import sys
sys.stdout = os.fdopen(sys.stdout.fileno(), 'w', 0)
# system
from datetime import datetime, timedelta
from functools import wraps
import pprint
import random
import re
import sys
import time
# pypi
import argh
import click
from cl... | metaperl/sbldr | src/main.py | Python | bsd-3-clause | 6,626 | [
"VisIt"
] | e11bc5e6f158f120d38cb3d30596f7431308264082ae48cabd2780715f057f18 |
#!/usr/bin/env python
import os
import sys
from collections import defaultdict
import sqlalchemy as sql
import numpy as np
from scipy.stats import mode
import pysam
import database
from gemini.annotations import annotations_in_region, annotations_in_vcf, guess_contig_naming
from gemini_windower import check_depe... | brentp/gemini | gemini/gemini_annotate.py | Python | mit | 14,016 | [
"pysam"
] | e4c293addac4f18f3422a76e36bb859c4dd348702962a811e54a3521424575a4 |
# -*- coding: utf-8 -*-
import sys
sys.path[0:0] = [""]
import bson
import os
import pickle
import unittest
import uuid
import weakref
from datetime import datetime
from bson import DBRef, ObjectId
from tests import fixtures
from tests.fixtures import (PickleEmbedded, PickleTest, PickleSignalsTest,
... | DavidBord/mongoengine | tests/document/instance.py | Python | mit | 99,399 | [
"exciting"
] | 90bbffed252f105d74d6e00ed2da93e4f5f7fdc90b9b0eaa0ca351f2c2e2369b |
# Orca
#
# Copyright 2005-2009 Sun Microsystems Inc.
# Copyright 2010-2011 Orca Team
# Copyright 2011-2015 Igalia, S.L.
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version ... | chrys87/orca-beep | src/orca/scripts/web/braille_generator.py | Python | lgpl-2.1 | 7,493 | [
"ORCA"
] | 0e8037eb1ca8e3776fbf62487faf73b277ec507676efce58c2918631ead76038 |
# Copyright (C) 2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later versio... | KaiSzuttor/espresso | testsuite/scripts/tutorials/test_06-active_matter__flow_field.py | Python | gpl-3.0 | 1,394 | [
"ESPResSo",
"VTK"
] | 94b15c29fe40da53f6c933d13e6ba0b7896da026a059745068ee2ce64d88dc83 |
#######################################################################
# #
# Copyright 2014 Cristian C Lalescu #
# #
# This file is part of py3Dpdf.... | chichilalescu/py3Dpdf | py3Dpdf/tvtk_tools.py | Python | gpl-3.0 | 4,329 | [
"VTK"
] | 6aec8876e5dc5b32b46ef3016cdcdb636a49a98b97ea12928993776ad441121d |
r"""
Ordination results format (:mod:`skbio.io.format.ordination`)
=============================================================
.. currentmodule:: skbio.io.format.ordination
The ordination results file format (``ordination``) stores the results of an
ordination method in a human-readable, text-based format. The form... | xguse/scikit-bio | skbio/io/format/ordination.py | Python | bsd-3-clause | 14,555 | [
"scikit-bio"
] | 319b4418863f9d311c61c48be28178ac5c9179031e9c50fad6096c330e56d4eb |
import types, os
import time
import math,struct
import statc
import string
import orngStat
import copy
import orngTest
import orange
import numpy
import commands
from statlib import stats
from AZutilities import miscUtilities
from AZutilities import dataUtilities
from rdkit import Chem
from rdkit.Chem import Draw
versi... | JonnaStalring/AZOrange | azorange/AZutilities/evalUtilities.py | Python | lgpl-3.0 | 44,470 | [
"RDKit"
] | 7503a2c10e16106f2b5739d59f2d8aa71fbb95932695a53de11cdf5cbf568996 |
# Hidden Markov Models
#
# Author: Ron Weiss <ronweiss@gmail.com>
# and Shiqiao Du <lucidfrontier.45@gmail.com>
# API changes: Jaques Grobler <jaquesgrobler@gmail.com>
"""
The :mod:`sklearn.hmm` module implements hidden Markov models.
**Warning:** :mod:`sklearn.hmm` is orphaned, undocumented and has known
numerical s... | johnowhitaker/bobibabber | sklearn/hmm.py | Python | mit | 48,255 | [
"Gaussian"
] | 82b395ed6bf36da280f555cbd6c234c33347ec240ffb8d3254d40aad58220703 |
from os.path import join
from os.path import dirname
import sys
import os
def addPeanoClawFlags(environment, build, libpath, libs, cpppath, cppdefines, ccflags, solver):
ccflags.append('-g3')
ccflags.append('-g')
if(environment['PLATFORM'] != 'darwin'):
ccflags.append('-march=native')
if solver=='... | unterweg/peanoclaw | tools/buildtools.py | Python | bsd-3-clause | 12,271 | [
"VTK"
] | c9cfbc7d613a18d244ea1f92182e0f161b96feb75ed90533c561b3cc4b990008 |
""" PDP
PDP ( PolicyDecisionPoint ) is the back-end for the PolicySystem. It discovers
the policies, finds the best match, evaluates them, merges their results taking
the most penalizing one, computes the set of actions to be triggered and returns
all the information to the PEP which will enforce the actions.
... | marcelovilaca/DIRAC | ResourceStatusSystem/PolicySystem/PDP.py | Python | gpl-3.0 | 15,502 | [
"DIRAC"
] | de5ec4870ac8938aaa05cd0dc359a11e1100c84909d31819d966b3a52fc2c14d |
##
# Copyright (C) 2012 Jasper Snoek, Hugo Larochelle and Ryan P. Adams
#
# This code is written for research and educational purposes only to
# supplement the paper entitled
# "Practical Bayesian Optimization of Machine Learning Algorithms"
# by Snoek, Larochelle and Adams
# Advances in Neural Information Processing... | recursix/spearmint-salad | spearmint_salad/spearmint/chooser/gp.py | Python | bsd-3-clause | 10,684 | [
"Gaussian"
] | 1ce780c04f0fcae70921902ab941e9662e830da11ca1423cf56bc640017b884a |
#!/usr/bin/env python3
# -*- coding: UTF-8 -*-
"""These classes deal with the Orca input and output structure."""
import os
import re
import sys
import numpy as np
from numpy import linalg
from .geometry import Geometry
from chemphysconst import Constants
# from . import systemtools as ST
TAB = " " * 4
FLOAT = np.floa... | jdcapa/MolecularToolbox | moleculartoolbox/orca.py | Python | gpl-3.0 | 33,803 | [
"ORCA"
] | 6d3aacad1c6d2d4d4ba1a25bd2d7df06454548c34184e1160a8c04749797a304 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkHyperOctreeDualGridContourFilter(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manage... | nagyistoce/devide | modules/vtk_basic/vtkHyperOctreeDualGridContourFilter.py | Python | bsd-3-clause | 528 | [
"VTK"
] | 2271d4334450d2ffee132eb5d728131f74276d5b08c6e15cf98fd62755ae324a |
# ##### BEGIN GPL LICENSE BLOCK #####
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distrib... | kellpossible/VoxelEditor | ScriptResearch/object_add_chain.py | Python | mit | 5,599 | [
"Brian"
] | edfb4088e609bf4e4f618b7f013a2a66216f4421938a6c31cbcc998f34eb4763 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Classes for reading/manipulating/writing VASP ouput files.
"""
import glob
import itertools
import json
import logging
import math
import os
import re
import warnings
import xml.etree.cElementTree as ET
fr... | gmatteo/pymatgen | pymatgen/io/vasp/outputs.py | Python | mit | 220,390 | [
"CRYSTAL",
"VASP",
"VisIt",
"Wannier90",
"pymatgen"
] | 4ae1873c7f1cab4d2057832d8cfcba7b02b7d1b4aa9a736f15ce6518b69fddc9 |
# sql/expression.py
# Copyright (C) 2005-2011 the SQLAlchemy authors and contributors <see AUTHORS file>
#
# This module is part of SQLAlchemy and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Defines the base components of SQL expression trees.
All components are derived ... | evensonbryan/yocto-autobuilder | lib/python2.7/site-packages/SQLAlchemy-0.7.0-py2.7-linux-x86_64.egg/sqlalchemy/sql/expression.py | Python | gpl-2.0 | 171,867 | [
"VisIt"
] | 4f64a16c04565fc67ca52893af878e534e9daeb882082024def0beb6ad7b636f |
"""Gaussian processes classification."""
# Authors: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
#
# License: BSD 3 clause
import warnings
from operator import itemgetter
import numpy as np
from scipy.linalg import cholesky, cho_solve, solve
from scipy.optimize import fmin_l_bfgs_b
from scipy.special import erf... | DailyActie/Surrogate-Model | 01-codes/scikit-learn-master/sklearn/gaussian_process/gpc.py | Python | mit | 31,610 | [
"Gaussian"
] | 8fc31bb1e88b4736006b834a3fb251f18b010550255d4317ea08f21754e8002b |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
urlpatterns = [
url(r'^$', TemplateView.as_view(templ... | nikkomidoy/yfc-social-site | config/urls.py | Python | bsd-3-clause | 1,232 | [
"VisIt"
] | 70243a1a9681c3aad1cb6290c8a1684e3fc0401470ff83a15abaaa343ddb77eb |
from __future__ import print_function
import unittest
from ann import ANN
class TestANN(unittest.TestCase):
def disabled( f):
def _decorator():
print(f.__name__ + ' has been disabled')
return _decorator
@disabled
def test_xor_trainig(self):
print("test_xor_trainig...")
nn = ANN([2, 2, 1])
inputs =... | Razvy000/ANN-Intro | test_ann.py | Python | mit | 4,712 | [
"NEURON"
] | 6764f0d92bd4ae83b2ce3de09a17ea1ae76f19a0c0df88fe1c1893f4794655b7 |
#!/usr/bin/python
from copy import copy, deepcopy
import sys
#from numpy import *
import numpy as np
# (c) 2015 Sandip De (1sandipde@gmail.com)
def main():
a=np.loadtxt('input.test')
# a=np.random.random((100,100))
costs=k_best_costs(20,a)
for x in costs:
print x
def k_best_costs(nbest,matrix):
#nbest: ... | sandipde/Hungarian-Murty | Hungarian-Murty-lowmem.py | Python | gpl-2.0 | 12,973 | [
"Brian"
] | b8d141a91787ba116acbc5fce66f49bdbf6536f39965191b9983c8f8a5007a83 |
# Copyright 2017 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | Xeralux/tensorflow | tensorflow/contrib/py2tf/converters/for_loops.py | Python | apache-2.0 | 3,089 | [
"VisIt"
] | e27747be5c7f1257c933c150ac8a657ee6040c0a77eb2692dceab1fb6007557e |
"""
This package implements the No-U-Turn Sampler (NUTS) algorithm 6 from the NUTS
paper (Hoffman & Gelman, 2011).
Content
-------
The package mainly contains:
nuts6 return samples using the NUTS
test_nuts6 example usage of this package
and subroutines of nuts6:
build_tree ... | mfouesneau/NUTS | nuts/nuts.py | Python | mit | 15,137 | [
"Gaussian"
] | 1a0fa6264f22ea8b90539ca05e9ed56d0085e4d423021d6d6bdcf71abfbcabfe |
"""
Functional GUI tests: run_basic() and run_detailed().
$Id$
"""
__version__='$Revision$'
import copy
from numpy import array
from numpy.testing import assert_array_equal
import topo
assert hasattr(topo,'guimain'), "GUI must be running."
import topo.tests.functionaltest as ft
from topo.tests.utils import assert... | jesuscript/topo-mpi | topo/tests/gui_tests.py | Python | bsd-3-clause | 6,333 | [
"Gaussian"
] | b92f52e10412212168bf04f705eb8746a3d765fc84faae30fee09903d10e9572 |
from django.db import models
from edc_appointment.models import AppointmentMixin
from edc_base.audit_trail import AuditTrail
from edc_base.model.models import BaseUuidModel
from edc_base.model.validators import (datetime_not_before_study_start, datetime_not_future,)
from edc_export.models import ExportTrackingFieldsMi... | botswana-harvard/microbiome | microbiome/apps/mb_maternal/models/antenatal_enrollment.py | Python | gpl-2.0 | 5,232 | [
"VisIt"
] | bee3330cb33d1f6acec9ad58ea650365d41942c28348ab242401413e78c57818 |
# Copyright 2008 by Bartek Wilczynski.
# Adapted from Bio.MEME.Parser by Jason A. Hackney. 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.
from __future__ import print_function
... | Ambuj-UF/ConCat-1.0 | src/Utils/Bio/motifs/mast.py | Python | gpl-2.0 | 4,913 | [
"Biopython"
] | 939e16a1420e746817b3e8e1e841c578938167b6e0865b216b8f2291f2455449 |
import idaapi
import threading
import time
wsserver = None
qira_address = None
# this handles all receiving
msg_queue = [] # python array is threadsafe
def handle_message_queue():
global msg_queue
while len(msg_queue) > 0:
dat = msg_queue[0].split(" ")
msg_queue = msg_queue[1:]
if dat[0] == "setadd... | KernelAnalysisPlatform/KlareDbg | ida/python/qira.py | Python | gpl-3.0 | 22,019 | [
"VisIt"
] | 114032c875914b1e486e371d836e6e06962985f5943654f8963665393e816468 |
# -*- coding: utf-8 -*-
"""
v1: Created on May 31, 2016
author: Daniel Garrett (dg622@cornell.edu)
"""
import numpy as np
import matplotlib.pyplot as plt
import FuncComp.Population as Population
import FuncComp.Functional as Functional
import FuncComp.MonteCarlo as MonteCarlo
import FuncComp.util as util
import time
... | dgarrett622/FuncComp | FuncComp/Plotting.py | Python | mit | 4,798 | [
"VisIt"
] | 6983dda05ddfb21b848bbbd19c7f0d02239dfe8e693a02a0e609927e98ae0a92 |
# Copyright 2007 by Tiago Antao <tiagoantao@gmail.com>. 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.
'''
Support for asynchronous execution.
'''
import os
import thread
... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/PopGen/Async/__init__.py | Python | apache-2.0 | 3,166 | [
"Biopython"
] | 689f3d62427e35ff06efcead27a36bd7dcaa1655d15cc0ffadc5cdbdb0e09e18 |
# -*- coding: utf-8 -*-
"""
Created on Sun Aug 14 14:53:28 2016
@author: Luciano Masullo, Federico Barabas
"""
import os
import numpy as np
import math
import configparser
from scipy.ndimage.measurements import center_of_mass
from skimage.feature import peak_local_max
try:
import skimage.filters as filters
except... | fedebarabas/ringfinder | ringfinder/tools.py | Python | gpl-3.0 | 17,415 | [
"Gaussian",
"NEURON"
] | 2b5a631f30289373bf98d30ad253c3c934a99697971bf7226107d9ab615f267d |
# -*- coding: utf-8 -*-
#
# Authors: Taylor Smith <taylor.smith@alkaline-ml.com>
# Jason White <jason.m.white5@gmail.com>
#
# The SMRT balancer
from __future__ import division, absolute_import, division
import numpy as np
from sklearn.preprocessing import LabelEncoder
from .base import _validate_X_y_ratio_c... | tgsmith61591/smrt | smrt/balance/smrt.py | Python | bsd-3-clause | 12,472 | [
"Gaussian"
] | fee944a8edaa00fb10023db335afd5d5cb0ecf701cbb8801af4a3ae21394c823 |
#!/usr/bin/env python
"""Convert pyx12 configuration files from XML to Python.
The Python X12 module contains a number of XML files which
define X12 message structures. They need to be converted into the syntax for the
:mod:`X12.parse` parser.
Note that the pyx12 module defines Loops, Segments, Composites and indivi... | sbuss/TigerShark | tigershark/tools/convertPyX12.py | Python | bsd-3-clause | 25,000 | [
"VisIt"
] | 9ab67b28f93256962d6ebeefe7c774ec49bce74f4fa8e222c2de277d3460056e |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageButterworthHighPass(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
... | nagyistoce/devide | modules/vtk_basic/vtkImageButterworthHighPass.py | Python | bsd-3-clause | 511 | [
"VTK"
] | cf1e5967b4f979575a51212dda48bb9dc98751ed5bc7ff3f8f5aa8883a2bc6cd |
#!/usr/bin/python2.7
# Copyright 2010 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | Byclosure/google-apis-client-generator | src/googleapis/codegen/api.py | Python | apache-2.0 | 52,242 | [
"VisIt"
] | 5554da42125ff0f804103d5b64058ba59dfa69a4ae3509a9cca37ae243d1c40e |
from __future__ import division
import os
import datetime
import sys
import urllib
import gzip
import pysam
from operator import itemgetter
# Class representing a transcript
class Transcript(object):
# Constructor
def __init__(self):
self.ENST = None
self.GENE = None
self.ENSG = None
... | RahmanTeam/CAVA | ensembldb/main.py | Python | mit | 19,497 | [
"pysam"
] | 855976b9919c3460aa89e41169c2bb919d451012d637bbe5fad487b0a5c91460 |
# -*- 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:
'''
Miscellaneous algorithms
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname(os.path.realpath(__file__))
>>> dat... | carolFrohlich/nipype | nipype/algorithms/misc.py | Python | bsd-3-clause | 48,574 | [
"Gaussian"
] | 3bd263545f1cf8c6b0cd31d75ebe515c903a2d2157e8ba2421301bba5dd2d407 |
# -*- coding: utf-8 -*-
#
# test_connect_helpers.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the Li... | magnastrazh/NEUCOGAR | nest/serotonin/research/C/nest-2.10.0/pynest/nest/tests/test_connect_helpers.py | Python | gpl-2.0 | 17,391 | [
"NEURON"
] | 6c6122c65ad062dcd366bfa4fcd70fe1e8ba6005ffd82680fef205ea82fc7523 |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the LMS.
"""
from datetime import datetime, timedelta
from flaky import flaky
from textwrap import dedent
from unittest import skip
from nose.plugins.attrib import attr
import pytz
import urllib
from bok_choy.promise import EmptyPromise
from common.test.acceptance.tests... | deepsrijit1105/edx-platform | common/test/acceptance/tests/lms/test_lms.py | Python | agpl-3.0 | 53,755 | [
"VisIt"
] | 3f4be3dfa011f75f7b7b57a863fdd8c8d73723552575e06c8d20ffb57115c5ba |
###############################################
# Snakemake rules associated with assembly
# blast, quast of a single subsample.
# this file must be included into another
# Snakemake file
###############################################
# rules
rule spade_assembly:
# order of the inputs are paired1 paired2 single1 ... | brianyu2010/Mini-Metagenomic_Analyses | Snakefile_subsample_assembly.py | Python | gpl-3.0 | 6,291 | [
"BLAST"
] | dde1d7c74d7dec934fa9d2256565b4a8733169a22d70aac94e98369cdd22fdea |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2007-2008 Brian G. Matherly
# Copyright (C) 2008 Gary Burton
#
# 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 ... | sam-m888/gprime | gprime/plug/menu/_text.py | Python | gpl-2.0 | 1,768 | [
"Brian"
] | 029c006eaa0a2355e00737e576a6d91ff29d15f6786c19df7267f8f6fdf09068 |
#!/usr/bin/env python3
class EspNoneType:
def __getattr__(self, name):
return self
def __str__(self):
return "none"
__repr__ = __str__
# Remove this when we stop making this mistake
def visit(self, v):
raise RuntimeError("none.visit()")
def __add__(self, other):
if not isinstance(other, str):
re... | ConsciousCode/espresso | src/runtime.py | Python | bsd-2-clause | 2,448 | [
"VisIt"
] | 47eedaca4953fa68cd3b0ad57448a2ece446ee440356a9b6e290af5a3befa700 |
"""
@name: Modules/House/Schedule/_test/test_sunrisesunset.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2011-2020 by D. Brian Kimmel
@note: Created on Mar 6, 2011
@license: MIT License
@summary: Calculate the suns location at local noon, then calculate sunrise and sun... | DBrianKimmel/PyHouse | Project/src/Modules/House/Schedule/_test/test_sunrisesunset.py | Python | mit | 7,197 | [
"Brian"
] | f929aa9c9fb5792a32b0388ac726382fa614ca89107a5c43dc9f825ef9cf6ad0 |
#!/usr/bin/env python
"""
author: bart aelterman
date: 2012-10-12
description: This class will help you find the taxonomy of a given BLAST hit
using its GI number. The taxon id is found for each GI number using the
GItaxidFinder class.
Next, for each taxon id, the taxonomy is fetched from the NCBI server using
... | bartaelterman/BlastTaxonomy | blasthittaxonomy.py | Python | mit | 2,602 | [
"BLAST",
"Biopython"
] | 77f0ad510253705298654c2816d0f91087b113ff1accf27ab95e9a3ef2bcd3ea |
##
# This file is an EasyBuild reciPY as per https://github.com/hpcugent/easybuild
#
# Copyright:: Copyright 2013-2014 CaSToRC, The Cyprus Institute
# Authors:: George Tsouloupas <g.tsouloupas@cyi.ac.cy>
# License:: MIT/GPL
# $Id$
#
##
"""
Easybuild support for building NAMD, implemented as an easyblock
@author: G... | omula/easybuild-easyblocks | easybuild/easyblocks/n/namd.py | Python | gpl-2.0 | 7,375 | [
"NAMD"
] | f995a69ea226d3ff2da9945c0479ba26dc6647bf79b11e2b5fc4657d8d87e724 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import argparse
import multiprocessing as mp
import os
import pysam
from datetime import datetime
from pynnotator import settings
from subprocess import run
class Dbnsfp(object):
def __init__(self, vcf_file=None):
self.vcf_file = vcf_file
... | raonyguimaraes/pynnotator | pynnotator/helpers/dbnsfp.snpsift.py | Python | bsd-3-clause | 1,541 | [
"pysam"
] | c72420c564e01719318de92b4fd1da959c911bb91b34631641bd22b84ca4e4e5 |
#
# Copyright 2014 James Kermode (Warwick U.)
#
# matscipy - Materials science with Python at the atomic-scale
# https://github.com/libAtoms/matscipy
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Founda... | libAtoms/matscipy | scripts/fracture_mechanics/quartz_crack.py | Python | lgpl-2.1 | 2,313 | [
"ASE",
"Matscipy"
] | b6af961047de8f88a9a25bd61c913d7899bc13538ca03d21c12f04952a451254 |
# This is a component for running a previoulsy-generated .idf file through EnergyPlus with a different weather file.
#
# Honeybee: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Honeybee.
#
# Copyright (c) 2013-2020, Mostapha Sadeghipour Roudsari <mostapha@... | mostaphaRoudsari/Honeybee | src/Honeybee_Re-run OSM.py | Python | gpl-3.0 | 13,774 | [
"EPW"
] | 9e10f7d704155146f13be12ecb70de3b901e9f22f7fa688134ed8749941701e0 |
"""
################################################################################
# Copyright (c) 2003, Pfizer
# Copyright (c) 2001, Cayce Ullman.
# Copyright (c) 2001, Brian Matthews.
#
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provid... | jjdmol/LOFAR | LTA/LTAIngest/SOAPpy-0.12.0/SOAPpy/Utilities.py | Python | gpl-3.0 | 5,093 | [
"Brian"
] | 89ab4a6ab8bfe718727c6791adca47db2cc9ad98c78783720b48d64946d0b615 |
# -*- mode: python; indent-tabs-mode: nil; c-basic-offset: 4; tab-width: 4; -*-
# vim: set shiftwidth=4 softtabstop=4 expandtab:
"""Support for reading meta-data and data NetCDF files, primarily
time-series data.
2014 Copyright University Corporation for Atmospheric Research
This file is part of the "django-ncharts"... | ncareol/ncharts | ncharts/netcdf.py | Python | bsd-2-clause | 49,418 | [
"NetCDF"
] | 0b7a32d250e07368baaafe356accbd679a888556b832e5caf480a0b916942240 |
# 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 PyUnicycler(PythonPackage):
"""Unicycler is an assembly pipeline for bacterial genomes. It... | LLNL/spack | var/spack/repos/builtin/packages/py-unicycler/package.py | Python | lgpl-2.1 | 1,554 | [
"BLAST"
] | 5ccd086c3d0ec8779d73accea54d30f0dc9543cc76ea28dde0610ac197fb30b2 |
#!/usr/bin/env python
# coding: utf-8
# # Inverse Problem: General Workflow and Examples
#
# In this example script, we'll reproduce many of the plots from the fitting release paper ([Conroy et al. 2020](http://phoebe-project.org/publications/2020Conroy+)).
#
# For the few figures not included here, see the followin... | phoebe-project/phoebe2-docs | development/examples/inverse_paper_examples.py | Python | gpl-3.0 | 19,902 | [
"Gaussian"
] | 384c1f04da4fe333a73a06f295a1e70bcbf5740410711002c58d1dd08014f4e6 |
#!/bin/env python
"""
Create and put 'PutAndRegister' request with a single local file
warning: make sure the file you want to put is accessible from DIRAC production hosts,
i.e. put file on network fs (AFS or NFS), otherwise operation will fail!!!
"""
import os
from DIRAC.Core.Base.Script import Script
... | DIRACGrid/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_put_and_register_request.py | Python | gpl-3.0 | 2,714 | [
"DIRAC"
] | 7d465c727bc18b98e3e0cdce6202841f82a3273dfe8cee0c970b5ff87ed198a2 |
import logging
import os
import os.path
import warnings
# os.environ['R_LIBS_USER'] = '/project/projectdirs/metatlas/r_pkgs/'
# curr_ld_lib_path = ''
from copy import deepcopy
from typing import Callable, List, Optional, Sized
from enum import Enum
from metatlas.datastructures import metatlas_objects as metob
from me... | biorack/metatlas | metatlas/plots/dill2plots.py | Python | bsd-3-clause | 156,022 | [
"RDKit"
] | c22c8ea659bfe3cee9751e97d3e5eb80bc287a0777f814973c2f6f0004dea384 |
__description__ = \
"""
Wrap BLAST for interfacing with phylopandas.
"""
__author__ = "Michael J. Harms (harmsm@gmail.com)"
__date__ = "2019-08-16"
import phylopandas as phy
# Modules for blasting, etc.
from Bio import SeqIO, Entrez
from Bio.Seq import Seq
from Bio.Blast import NCBIWWW, NCBIXML
import Bio.Blast.Appli... | Zsailer/phylo_tools_2 | phylogenetics/tools/blast.py | Python | unlicense | 3,854 | [
"BLAST"
] | 73491c730d721eac2b6d0b1798b0c4a464e64ab168f8dcf82dddcbda5dfcd21c |
"""Competitions for parameter tuning using the cross-entropy method."""
from __future__ import division
from random import gauss as random_gauss
from math import sqrt
from gomill import compact_tracebacks
from gomill import game_jobs
from gomill import competitions
from gomill import competition_schedulers
from gomi... | inclement/noGo | noGo/ext/gomill/cem_tuners.py | Python | gpl-3.0 | 18,960 | [
"Gaussian"
] | 587a7f16447ab1607ea55f3b623e89dadf046bae5db0ec905df742138ae0e022 |
# The OARN Relief Nursery Database
# Copyright (C) 2015 Oregon Association of Relief Nurseries
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at... | wire-rabbit/oarn-database | oarndb/views/reference_views.py | Python | agpl-3.0 | 36,179 | [
"VisIt"
] | db44e70ba156c44a7864b176ce4babc862f590682b217554e5f255d511d2e92f |
# -*- Mode: Python; coding: utf-8; indent-tabs-mode: nil; tab-width: 4 -*-
### BEGIN LICENSE
# Copyright (C) 2014 Brian Douglass bhdouglass@gmail.com
# This program is free software: you can redistribute it and/or modify it
# under the terms of the GNU General Public License version 3, as published
# by the Free Softwa... | bhdouglass/agui | agui/aextras/icon.py | Python | gpl-3.0 | 1,266 | [
"Brian"
] | e6515f29ba5ef29a3ffc4028338ae289b3db97c01a9a907f6854133f1714031d |
from lsst.obs.decam.ingest import DecamParseTask
config.parse.retarget(DecamParseTask)
config.parse.translation = {'visit': 'EXPNUM',
'taiObs': 'DATE-OBS',
'expTime': 'EXPTIME',
'ccdnum': 'CCDNUM', # MEF header layer
... | lsst/obs_decam | config/ingest.py | Python | gpl-3.0 | 1,988 | [
"VisIt"
] | 44eed725de16b86e21ffd617673817a09bf495dce2548b9b0756cf8235013e06 |
from .estimator_base import H2OEstimator
class H2OGeneralizedLinearEstimator(H2OEstimator):
def __init__(self, model_id=None, max_iterations=None, beta_epsilon=None, solver=None,
standardize=None, family=None, link=None, tweedie_variance_power=None,
tweedie_link_power=None, alpha=None,... | nilbody/h2o-3 | h2o-py/h2o/estimators/glm.py | Python | apache-2.0 | 10,502 | [
"Gaussian"
] | f2ab41d0c6325d53e522315c5f3de37932cbf3d0570c36a9efff2bd8be8dfa27 |
#!/usr/bin/python
#Audio Tools, a module and set of tools for manipulating audio data
#Copyright (C) 2008-2012 Brian Langenberger
#This program is free software; you can redistribute it and/or modify
#it under the terms of the GNU General Public License as published by
#the Free Software Foundation; either version 2... | Excito/audiotools | audiotools/cue.py | Python | gpl-2.0 | 15,200 | [
"Brian"
] | 47550cac83388a6f39facefeb6aeadfbfbff17a318d1cda61138687990fdaff3 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from __future__ import unicode_literals
from builtins import str
from builtins import range
from builtins import open
from future.moves.urllib.request import urlopen
from future.moves.urllib.parse import urlpars... | migeruhito/sagenb | sagewui/blueprints/worksheet.py | Python | gpl-3.0 | 53,863 | [
"Jmol"
] | aa4b8672c9b68c2201900443c911c1f74a4d8a8d3bf677ad9ab25ee748d173e7 |
# 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 Openbabel(CMakePackage):
"""Open Babel is a chemical toolbox designed to speak the many la... | LLNL/spack | var/spack/repos/builtin/packages/openbabel/package.py | Python | lgpl-2.1 | 2,783 | [
"Open Babel",
"Pybel"
] | be2556e7fcb257a9c3be55b1d2d1023d754e004976fd3d621fde6ff138cdc776 |
"""
Tests the ComponentMonitoring DB and Service by creating, checking,
updating and removing several instances of each table in the DB
This program assumes that the service Framework/ComponentMonitoring is running
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_f... | ic-hep/DIRAC | tests/Integration/Framework/Test_InstalledComponentsDB.py | Python | gpl-3.0 | 13,980 | [
"DIRAC"
] | 65e867080b61ea1196558a8b67dfb801499a8d684e7f658690b480496b115383 |
# coding: utf-8
# ### Getting started with Docker
#
#
# This notebook demonstrates docker for the gis image that I've uploaed to [dockerhub](https://hub.docker.com/r/phaustin/gis/)
#
# Major benefit: The installation should "just work" with no package conflicts. Like github, dockerhub
# has become a center for ... | a301-teaching/a301_code | notebooks/python/docker_demo.py | Python | mit | 1,560 | [
"VisIt"
] | 5c10bba1192d86a5d2ea1c323fca51853c4159116cfb7ed85f9e160aefc5885d |
# coding=utf-8
"""
This module provides a class :class:`~BioGrid`.
.. topic:: What is BioGrid ?
:URL: http://thebiogrid.org/
:REST: http://wiki.thebiogrid.org/doku.php/biogridrest
.. highlights::
BioGRID is an online interaction repository with data compiled through
comprehensive curatio... | ArnaudKOPP/BioREST | BioREST/Biogrid.py | Python | gpl-3.0 | 13,391 | [
"VisIt"
] | 09551a6355e272308cd670e0520f25ebf058e131abe3389e2546e4ddbcd62d47 |
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