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import math
import chainer
import chainer.functions as F
import numpy as np
from chainer import cuda, Variable
from scipy.fftpack import dct, idct
from scipy.ndimage import correlate
from scipy.optimize import minimize
from skimage.filters import gaussian, sobel_h, sobel_v, scharr_h, scharr_v, roberts_pos_diag, robert... | wuhuikai/GP-GAN | gp_gan.py | Python | mit | 7,602 | [
"Gaussian"
] | 9a7f5d8ec8f9a6fc36e117126134b7443fc4dbf941b196e84ea6a309276cf455 |
#
# Copyright (c) 2017 Intel Corporation
# SPDX-License-Identifier: BSD-2-Clause
#
from __future__ import print_function, division, absolute_import
import sys
import numpy as np
import ast
import inspect
import operator
import types as pytypes
from contextlib import contextmanager
from copy import deepcopy
import nu... | jriehl/numba | numba/tests/test_stencils.py | Python | bsd-2-clause | 95,948 | [
"VisIt"
] | 7f66e7d5ac6d26fecb786aa67d202573002a999e99b9482a1dbce8cd9e2a4702 |
from __future__ import unicode_literals
import json
import logging
import re
from itertools import chain
import dateutil.parser
from django.conf import settings
from django.contrib.sites.models import Site
from django.core.exceptions import MultipleObjectsReturned, ObjectDoesNotExist
from django.db.models import Q
fr... | brennie/reviewboard | reviewboard/reviews/views.py | Python | mit | 83,117 | [
"VisIt"
] | f5c16cd4ca3dda98b63fda07a0aa5015f987e1f17c27f6a936f2951268bd828f |
from __future__ import division
import numpy as np
import paraBEM
from paraBEM.pan2d import doublet_2_0, doublet_2_0_v, source_2_0, source_2_0_v
from paraBEM.vtk_export import VtkWriter
from paraBEM.utils import check_path
R = 1
points = [
[-2, -2], [2, -2], [2, 2], [-2, 2],
[-1, -1], [1, -1], [1, 1], [-1, 1]... | looooo/paraBEM | examples/vtk/heat_ring.py | Python | gpl-3.0 | 1,814 | [
"VTK"
] | 45f9ae37fdf4ca7b306c2a1095f40f2bfe0d6477ac597cd1ddf37e74e484861d |
"""
Contains BACE data loading utilities.
"""
from __future__ import print_function
from __future__ import division
from __future__ import unicode_literals
import sys
import os
import deepchem
import tempfile
import deepchem as dc
from deepchem.molnet.load_function.bace_features import bace_user_specified_features
d... | miaecle/deepchem | examples/bace/bace_datasets.py | Python | mit | 2,638 | [
"CRYSTAL"
] | 4de191b10cdaf23d0833664895bb51248c17036fc44800cb02a07c0bc6368dee |
'''
This file takes a cleaned SPF csv file and makes csv file with measures of
individual uncertainty
'''
import os
import pandas as pd
import scipy.stats as stats
import scipy.optimize as opt
import numpy as np
def fit_normal_to_hist(h):
'''
This function fits a gausian distribution to a histogram
... | BadWizard/Inflation | SPF/source/get_individ_uncert_spf.py | Python | mit | 4,523 | [
"Gaussian"
] | 6ca03dddae869473df6a8e1b92079ceca2facff9acb9917cc2f4bcb6562d30a2 |
# Copyright (c) Facebook, Inc. and its affiliates.
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2.
import collections
import itertools
import os
import re
import shutil
import sys
from bindings import nodemap
from dulwich import client, config as dul... | facebookexperimental/eden | eden/hg-server/edenscm/hgext/hggit/git_handler.py | Python | gpl-2.0 | 71,253 | [
"Octopus"
] | 323a791aa17a67a45ecffb60fcc18fb932d8bbe0a9df1f383e4e2e83a33146d5 |
""" Models for the shopping cart and assorted purchase types """
from collections import namedtuple
from datetime import datetime
from datetime import timedelta
from decimal import Decimal
import analytics
from io import BytesIO
import pytz
import logging
import smtplib
import StringIO
import csv
from boto.exception i... | chudaol/edx-platform | lms/djangoapps/shoppingcart/models.py | Python | agpl-3.0 | 74,561 | [
"VisIt"
] | 9f78230db8bf3d44de4b85e0b50ab944711b024fac002164da106c8393d7f4c4 |
# AvsP - an AviSynth editor
#
# Copyright 2007 Peter Jang <http://avisynth.nl/users/qwerpoi>
# 2010-2017 the AvsPmod authors <https://github.com/avspmod/avspmod>
#
# 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
#... | AvsPmod/AvsPmod | setup.py | Python | gpl-2.0 | 9,077 | [
"VisIt"
] | 87abb3909ceb38cab262cf6c21a54dac50f20c3d74116e19e5284aeb0aaf9f8c |
"""
Django settings for pyconuk project.
Generated by 'django-admin startproject' using Django 1.9.6.
For more information on this file, see
https://docs.djangoproject.com/en/1.9/topics/settings/
For the full list of settings and their values, see
https://docs.djangoproject.com/en/1.9/ref/settings/
"""
import os
#... | nanuxbe/2017.pyconuk.org | pyconuk/settings.py | Python | mit | 3,236 | [
"Amber"
] | e50ac2d07cc06e57d07d5f067a3094139dbe0e614433c46a61e5e9a21af33919 |
#!/usr/bin/env python
import sys
import pylibdmtx
SCRIPTS = ['read_datamatrix', 'write_datamatrix']
# Optional dependency
PILLOW = 'Pillow>=3.2.0'
URL = 'https://github.com/NaturalHistoryMuseum/pylibdmtx/'
def readme():
# TODO IOError on Python 2.x. FileNotFoundError on Python 3.x.
try:
with open... | NaturalHistoryMuseum/pylibdmtx | setup.py | Python | mit | 2,315 | [
"VisIt"
] | 2f8bef830bd15e13050f7891d6315c453c8e312e5449ce5013a9f873cc721e4e |
#!/usr/bin/env python3
# calibrate.py
""" assists with calibration of MAXN_STORAGE parameter,
which is the most important parameter regarding server performance.
"""
import argparse
import os
import glob
import gzip
from Bio import SeqIO
import numpy as np
import scipy.special
from bokeh.layouts import gridplot
fro... | davidhwyllie/findNeighbour2 | src/calibrate.py | Python | lgpl-3.0 | 3,089 | [
"Biopython"
] | c62c3c7ec839381099e3adb22fd02c89d184376c383808dabf63f5d013f4e3b3 |
#Just a copy of the version in python 2.5 to be used if it's not available in jython 2.1
"""Simple XML-RPC Server.
This module can be used to create simple XML-RPC servers
by creating a server and either installing functions, a
class instance, or by extending the SimpleXMLRPCServer
class.
It can also be used to hand... | dannyperry571/theapprentice | script.module.pydevd/lib/_pydev_imps/_pydev_SimpleXMLRPCServer.py | Python | gpl-2.0 | 21,765 | [
"Brian"
] | 72280522ccc7a1a89d7fe859fbef45a63fc371e25aa30fab6cd3f9886b6ee3e1 |
from helpers import compute_volume
import pygmsh
def test():
with pygmsh.geo.Geometry() as geom:
poly = geom.add_polygon(
[[0.0, 0.5], [1.0, 0.5], [1.0, 1.0], [0.0, 1.0]],
mesh_size=0.05,
)
cp = geom.copy(poly)
geom.symmetrize(cp, [0.0, 1.0, 0.0, -0.5])
... | nschloe/pygmsh | tests/built_in/test_symmetrize.py | Python | gpl-3.0 | 504 | [
"VTK"
] | 70b2ab0c4a05e57d77252393b9784bb2d752229ef7d0b0c5c299cd08fb7ae54a |
########################################################################
# File : ComputingElement.py
# Author : Stuart Paterson, A.T.
########################################################################
""" The Computing Element class is a base class for all the various
types CEs. It serves several purpos... | ic-hep/DIRAC | src/DIRAC/Resources/Computing/ComputingElement.py | Python | gpl-3.0 | 22,117 | [
"DIRAC"
] | 4906be7af3de8e626e09eead2abb2fd1e278b683a02721c66f7ecb4262c8ad70 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | fweik/espresso | testsuite/python/lb_thermostat.py | Python | gpl-3.0 | 2,652 | [
"ESPResSo"
] | e117687d93899d07cb1104426c43862af67e31c371e890dff062644e4b4977ba |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import scipy.io
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
imp... | tapomayukh/projects_in_python | sandbox_tapo/src/skin_related/AI_Surface_Recognition/src/hmm_crossvalidation_force_1_states.py | Python | mit | 14,805 | [
"Gaussian",
"Mayavi"
] | d5f1615e756656428bfb79643ed47b4311b0f33bd0a5dfd4feccb68e065d0639 |
# -*- 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... | tanmaykm/edx-platform | common/test/acceptance/tests/lms/test_lms.py | Python | agpl-3.0 | 53,757 | [
"VisIt"
] | c7622afed1e7233e7adf0e0f9545e19011cf7da9334e3a026db659a0a10b5f92 |
# 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 Nco(AutotoolsPackage):
"""The NCO toolkit manipulates and analyzes data stored in
netC... | iulian787/spack | var/spack/repos/builtin/packages/nco/package.py | Python | lgpl-2.1 | 2,993 | [
"NetCDF"
] | 66e5f8d7b28f79614f29ccab5b2d9142fe71e79b3f58f02429150b88e956ac5a |
##
## Biskit, a toolkit for the manipulation of macromolecular structures
## Copyright (C) 2004-2012 Raik Gruenberg
##
## 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
... | ostrokach/biskit | Biskit/atomCharger.py | Python | gpl-3.0 | 10,365 | [
"Amber"
] | 99aa1cd5d2b46a358c4832db3a563eb509ec0fe6f2179fe4799c99fda7e7f9e1 |
from unittest import TestCase
from dark.hsp import HSP, LSP
class TestHSP(TestCase):
"""
Tests of the L{dark.hsp.HSP} class.
"""
def testExpectedAttributes(self):
"""
An HSP must have the expected attributes.
"""
hsp = HSP(7, readStart=1, readEnd=2,
... | bamueh/dark-matter | test/test_hsp.py | Python | mit | 3,533 | [
"BLAST"
] | a6f60e9b93f33343942b1271b80d1dd51b3c93df3d891e6e0dceae875fbc31f4 |
import os
import re
import json
from Bio.Seq import Seq
from edge.blast import blast_genome
from edge.models import Fragment, Operation
from edge.primer import design_primers_from_template
from edge.pcr import pcr_from_genome
from edge.orfs import detect_orfs
SINGLE_CROSSOVER_MAX_GAP = 2000
MAX_INTEGRATION_SIZE = 5... | ginkgobioworks/edge | src/edge/recombine.py | Python | mit | 29,056 | [
"BLAST"
] | e60f431c6fd0b5ed33191de047da9ed58dbb8f8de8941b504a542e7c3b349dc8 |
# Orca
#
# Copyright 2004-2009 Sun Microsystems Inc.
# Copyright 2010-2013 The Orca Team
#
# This library is free software; you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation; either
# version 2.1 of the License, or (at your... | pvagner/orca | src/orca/cmdnames.py | Python | lgpl-2.1 | 53,172 | [
"ORCA"
] | 59e27dd083517d05be28062f8ad7ed6691a719406a3923e5681473741b665a92 |
"""Read genome build configurations from Galaxy *.loc and bcbio-nextgen resource files.
"""
import ConfigParser
import glob
import os
import sys
from xml.etree import ElementTree
import toolz as tz
import yaml
from bcbio import utils
from bcbio.distributed import objectstore
from bcbio.log import logger
from bcbio.ng... | hjanime/bcbio-nextgen | bcbio/pipeline/genome.py | Python | mit | 13,597 | [
"Galaxy"
] | 3f8969e6338f9d148e80b87332f7d49ee1788c0d17b8d4a64bf305ddde2764d8 |
import unittest
from streamsx.topology.topology import *
from streamsx.topology import context
from streamsx.topology.schema import CommonSchema, StreamSchema
from streamsx.topology.tester import Tester
from streamsx.spl import op
import time
import os
import datetime
def _delay(x):
time.sleep(0.2)
return x
... | ddebrunner/streamsx.topology | test/python/topology/test2_python_window.py | Python | apache-2.0 | 10,778 | [
"DIRAC"
] | c67b4cf23ce0c26f58bec58f8088660208194699a293dfda0e4c4e6472f1e158 |
#~~~~~~~GLOBAL IMPORTS~~~~~~~#
# Third party package import
from Bio import pairwise2
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
class PairwiseAligner(object):
"""
@class PairwiseAligner
@brief Require the third party package Biopython
"""
... | a-slide/pyDNA | FastqFT/PairwiseAligner.py | Python | gpl-2.0 | 2,932 | [
"Biopython"
] | 0b6f3d1b4c4d956e60eff603e3c1b19f06d92977d1fe558b47c80a01d694df7e |
# Copyright 2014 Alistair Muldal <alistair.muldal@pharm.ox.ac.uk>
# 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 your option) any later version.
# Th... | orlandi/connectomicsPerspectivesPaper | participants_codes/konnectomics/fakedata/fake_blur.py | Python | mit | 2,691 | [
"Gaussian"
] | ce6ff2484f8ee8cf54526ec850a5adb84c1b3058800ac37623d887a5a5583b85 |
# Copyright 2009 by Cymon J. Cox. 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.
"""Command line wrapper for the multiple alignment programme MAFFT.
http://align.bmr.kyushu-u.a... | BlogomaticProject/Blogomatic | opt/blog-o-matic/usr/lib/python/Bio/Align/Applications/_Mafft.py | Python | gpl-2.0 | 16,403 | [
"BLAST",
"Biopython"
] | b5f7359378784a56dca121d8c27056d8ba987d162836b3e35d3e8bca2ffa7fa0 |
# PD is a free, modular C++ library for biomolecular simulation with a
# flexible and scriptable Python interface.
# Copyright (C) 2003-2013 Mike Tyka and Jon Rea
#
# 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... | mtyka/pd | examples/rotamer/rotamer_library_io/run.py | Python | gpl-3.0 | 3,097 | [
"CHARMM"
] | 1c1a508390d57e1ed673eb116888109828bd51e126b840324b30d8c53699cfeb |
#!/usr/bin/env python
##############################################################################################
#
#
# CMIP6_hybrid_regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://... | acsis-project/emissions | emissions/python/CMIP6_hybrid/CMIP6_hybrid_regrid_C2H6_emissions_n96e_360d.py | Python | gpl-3.0 | 17,551 | [
"NetCDF"
] | 53004ae153e67c22c2deccda7e9034deaab79ef0d4ea8f99cdb31f7dda34bcf0 |
# Copyright 2017 Joachim van der Herten
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in wr... | GPflow/GPflowOpt | gpflowopt/acquisition/acquisition.py | Python | apache-2.0 | 18,067 | [
"VisIt"
] | f6a96852fd94f6d393075a74b28afe47d68f2700d7edf7dc15cc57156a3ec282 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import numpy
import unittest
import sys
sys.path.append('.')
from chempy.species import Species, TransitionState
from chempy.reaction import *
from chempy.states import *
from chempy.kinetics import ArrheniusModel
from chempy.thermo import WilhoitModel
##################... | jwallen/ChemPy | unittest/reactionTest.py | Python | mit | 6,118 | [
"ChemPy"
] | 9302e6043fc8ebc32b236e1e8013db545405df0dc09ff35ffccd3e833f01ed56 |
"""Main Lomb-Scargle Implementation"""
import numpy as np
from .implementations import lombscargle, available_methods
from .implementations.mle import periodic_fit, design_matrix
from . import _statistics
from astropy import units
from astropy.time import Time, TimeDelta
from astropy import units as u
from astropy.ti... | stargaser/astropy | astropy/timeseries/periodograms/lombscargle/core.py | Python | bsd-3-clause | 28,613 | [
"Gaussian"
] | 1c778c32d012b361f23a3a8f04d71be84d6870667719b65db11644b489f4d7e3 |
"""
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 your option) any later version.
Written (W) 2013 Heiko Strathmann
Written (W) 2013 Dino Sejdinovic
"""
imp... | karlnapf/kameleon-mcmc | kameleon_mcmc/tests/StandardMetropolisTest.py | Python | bsd-2-clause | 1,859 | [
"Gaussian"
] | fd48cea28abb9ebda3fd88c2f9943fd4813fbc79b237e8136d0284c05b0b03a8 |
########################################################################
# File : SSHComputingElement.py
# Author : Dumitru Laurentiu
########################################################################
""" SSH (Virtual) Computing Element: For a given list of ip/cores pair it will send jobs
directly through ... | miloszz/DIRAC | Resources/Computing/SSHBatchComputingElement.py | Python | gpl-3.0 | 7,481 | [
"DIRAC"
] | 8ba5037fb8e8b845f35e6fbc92823908a3bbf14a236ca6f9f86add0228bf39a6 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2021, the cclib development team
#
# This file is part of cclib (http://cclib.github.io) and is distributed under
# the terms of the BSD 3-Clause License.
"""Generate the coverage.rst and coverage.rst files from test results."""
import os
import sys
from docs_common import c... | cclib/cclib | doc/sphinx/coverage.py | Python | bsd-3-clause | 4,494 | [
"ADF",
"Dalton",
"GAMESS",
"Gaussian",
"Jaguar",
"Molpro",
"NWChem",
"ORCA",
"cclib"
] | ebf29d6c772eafd961c6a5ea9e299005b9e890ead45e765edd3859de77f3aa27 |
import warnings
warnings.warn("pymatgen.phasediagram.pdmaker has been moved pymatgen.phasediagram.maker. This stub "
"will be removed in pymatgen 4.0.", DeprecationWarning)
from .maker import *
| Bismarrck/pymatgen | pymatgen/phasediagram/pdmaker.py | Python | mit | 208 | [
"pymatgen"
] | a8a4bb49963a1334703fe11ec52a5e21d36a04325d287eb73a3b459ae44b2412 |
#!/usr/bin/env python
"""
Create a DIRAC MoveReplica request to be executed by the RMS
Usage:
dirac-dms-move-replica-request [options] ... sourceSE LFN targetSE1 [targetSE2...]
Arguments:
sourceSE: source SE
targetSE: target SE
LFN: LFN or file containing a List of LFNs
"""
from __future__ import a... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/scripts/dirac_dms_move_replica_request.py | Python | gpl-3.0 | 3,761 | [
"DIRAC"
] | 27427472dc12f1ec56169eec17c14d082f0154916afe4cd83e17742c9fff3ee8 |
#!/usr/bin/python2
#NOTE: Run this plot script from directory deft/papers/fuzzy-fmt
#with comand ./new-melting_miniplot_script.py [directory where data stored] [temp]
#to create plots from plot.dat files already in the data directory
import os
import numpy as np
import matplotlib.pyplot as plt
import sys
import matpl... | droundy/deft | papers/fuzzy-fmt/new-melting_miniplot_script.py | Python | gpl-2.0 | 1,843 | [
"CRYSTAL"
] | 9f48befac1de13ca298451be15932fb96f879b33ee947a3d6977d35327f27894 |
"""
Base module for processing all timeseries based data.
Use this as the base module for processing illfiles,bf.txt,weafiles.
Dependencies: none
Python version : 2.7
"""
from __future__ import print_function
from __future__ import division
import logging
logger = logging.getLogger("__main__")
logging... | sariths/stadicViewer | StadicViewer/gui/dataStructures/timeSeries.py | Python | mit | 3,404 | [
"EPW"
] | b2cac448111a43e835da32cec7c83521cd0f47e68392c80448d97fda53e81b07 |
# Created by G. Peter Lepage (Cornell University) in 12/2013.
# Copyright (c) 2013-21 G. Peter Lepage.
#
# 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
# any... | gplepage/vegas | tests/test_vegas.py | Python | gpl-3.0 | 50,174 | [
"Gaussian"
] | 44c9cc905c0b13d5073a60ace10e5952abf86856c9309e07fac01a520af60e6a |
# flake8: noqa
# Version: 0.18
"""The Versioneer - like a rocketeer, but for versions.
The Versioneer
==============
* like a rocketeer, but for versions!
* https://github.com/warner/python-versioneer
* Brian Warner
* License: Public Domain
* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy
* [![L... | chunweiyuan/xarray | versioneer.py | Python | apache-2.0 | 68,628 | [
"Brian"
] | e86fb63766cdbd98b353d98a23c8e311ca6d8bf7fabdc16ef4d711f20dc4e888 |
# A simple CLI runner for slurm that can be used when running Galaxy from a
# non-submit host and using a Slurm cluster.
from logging import getLogger
try:
from galaxy.model import Job
job_states = Job.states
except ImportError:
# Not in Galaxy, map Galaxy job states to Pulsar ones.
from pulsar.util im... | galaxyproject/pulsar | pulsar/managers/util/cli/job/slurm.py | Python | apache-2.0 | 2,941 | [
"Galaxy"
] | f6b1ea604fb4518ca22048baefabb784596b3f4c7eb30f4cd92a941b5dc58677 |
"""
Project
FPGA-Imaging-Library
Design
LightnessTransform
Function
Change the lightness of an image.
Module
Software simulation.
Version
1.0
Modified
2015-05-16
Copyright (C) 2015 Dai Tianyu (dtysky)
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser Gener... | wamgoo/FPGA-Imaging-Library | Point/LightnessTransform/SoftwareSim/sim.py | Python | lgpl-2.1 | 2,927 | [
"MOE"
] | 484257a553663c141401408a8f71ee46f31545eb79e93fb0738953493f566fef |
from octopus.core import app
from octopus.lib import http
import urllib, string
from lxml import etree
from octopus.modules.epmc import models
def quote(s, **kwargs):
try:
return urllib.quote_plus(s, **kwargs)
except:
pass
try:
utf = s.encode("utf-8")
return urllib.quote(ut... | JiscPER/magnificent-octopus | octopus/modules/epmc/client.py | Python | apache-2.0 | 3,284 | [
"Octopus"
] | a7d4b1e5bf3f36059868492050dc16a0d244fe5236fcafe9f1188583c8581648 |
#!/usr/bin/env python
# encoding: utf-8
'''
Created by Brian Cherinka on 2016-04-08 14:31:34
Licensed under a 3-clause BSD license.
Revision History:
Initial Version: 2016-04-08 14:31:34 by Brian Cherinka
Last Modified On: 2016-04-08 14:31:34 by Brian
'''
from __future__ import print_function
from __future__... | albireox/marvin | python/marvin/web/controllers/galaxy.py | Python | bsd-3-clause | 25,513 | [
"Brian",
"Galaxy"
] | 55db1a5013199627a4d5601d9d234f4727d49a8fcdc9988c6ff3f5df5d9084e4 |
# ceb.po
val = {" days." : "",
"(all)" : "",
"(any)" : "",
"(anyone)" : "",
"(available)" : "",
"(blank)" : "",
"(both)" : "",
"(everyone)" : "",
"(master user, not editable)" : "",
"(no change)" : "",
"(no deduction)" : "",
"(none)" : "",
"(unknown)" : "",
"(use system)" : "",
"({0} given, {1} remaining)" : "",
"1 tr... | bobintetley/asm3 | src/asm3/locales/locale_ceb.py | Python | gpl-3.0 | 108,559 | [
"Amber",
"VisIt"
] | e61d50a10b8a9813e15d48021d298d7f8dd59e686773363c2aea5799b19ff260 |
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 time,re,logging
import math
from T... | mtthwflst/terse | Parsers/NBO.py | Python | mit | 12,904 | [
"Gaussian"
] | cf7180165f32db4bf8cafc3a302e7a9345088be09d03b000f2f5f78aa0e9e79b |
#!/usr/bin/env python
# Copyright 2014-2019 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/pbc/cc/eom_kccsd_rhf_ip.py | Python | apache-2.0 | 2,429 | [
"PySCF"
] | cecfb46d475f44741e15cfd334af4606800c16a263321632b6758d5631285899 |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
import peac... | nuclear-wizard/moose | python/peacock/PostprocessorViewer/plugins/PostprocessorPlugin.py | Python | lgpl-2.1 | 2,454 | [
"MOOSE"
] | 02627e7213e17b91599e300d70d4f6951125b07daa8992ad4656b145ff863c30 |
# Copyright 2019 IBM. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed t... | CODAIT/graph_def_editor | tests/graph_test.py | Python | apache-2.0 | 22,332 | [
"VisIt"
] | 52d05d1f878207eb6f3bc0e8aa0339d6af5290c3857bf5bf6d50479af2ccfa21 |
import gensim
from gensim import models
from rdkit import Chem
from rdkit.Chem import rdMolDescriptors
import numpy as np
def main() :
model = models.KeyedVectors.load_word2vec_format("vec.txt")
embeddings = list()
# Using canonical smiles for glycine, as in original research paper
mol = Chem.MolFromS... | Agent007/deepchem | contrib/mol2vec/eval_mol2vec_results.py | Python | mit | 763 | [
"RDKit"
] | 1877ded35edad3af0f4e27ec13815444998adefd36a762f2a11596a8163e69d7 |
"""DFTB+ calculator interface."""
# Copyright (C) 2015 Atsushi Togo
# All rights reserved.
#
# This file is part of phonopy.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
#
# * Redistributions of source code must re... | atztogo/phonopy | phonopy/interface/dftbp.py | Python | bsd-3-clause | 6,665 | [
"VASP",
"phonopy"
] | e79e41579fe5a76cb8ebef11ae8b50e8cbe29c92c883e3b567db5a07a1d438ac |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2004-2009 Edgewall Software
# Copyright (C) 2004 Daniel Lundin <daniel@edgewall.com>
# Copyright (C) 2004-2006 Christopher Lenz <cmlenz@gmx.de>
# Copyright (C) 2006 Jonas Borgström <jonas@edgewall.com>
# Copyright (C) 2008 Matt Good <matt@matt-good.net>
# All rights reserved.
#... | dokipen/trac | trac/web/session.py | Python | bsd-3-clause | 11,069 | [
"VisIt"
] | 6d4d27e47b853fbc061b1eca673e288507be7b3d94c85e61ff6d8d90bfe7df2a |
# coding=utf-8
from __future__ import division
import numpy as _np
from scipy.signal import welch as _welch, periodogram as _periodogram, freqz as _freqz
import scipy.optimize as _opt
from scipy import linalg as _linalg
import itertools as _itertools
from ..BaseTool import Tool as _Tool
from ..Signal import UnevenlySi... | MPBA/pyphysio | pyphysio/tools/Tools.py | Python | gpl-3.0 | 50,287 | [
"Gaussian"
] | 8b2296ba6ad8d5393b952f95476dbf17f72106c4db45cffb1c9718eed7c84be9 |
from djblets.testing.decorators import add_fixtures
from djblets.webapi.errors import DOES_NOT_EXIST
from reviewboard.accounts.models import ReviewRequestVisit
from reviewboard.webapi.resources import resources
from reviewboard.webapi.tests.base import BaseWebAPITestCase
from reviewboard.webapi.tests.mimetypes import ... | reviewboard/reviewboard | reviewboard/webapi/tests/test_archived_review_request.py | Python | mit | 4,662 | [
"VisIt"
] | f8c71c21c9622079a15e20d29f68074df18cf8623b52a654bc17c3cec6818cf9 |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/tdscf/uks.py | Python | apache-2.0 | 8,871 | [
"PySCF"
] | a49f48b1467729510a77bdee19562b364c9782160894961eb530cda27d030a08 |
#
# Copyright 2014, 2020 James Kermode (Warwick U.)
# 2020 Arnaud Allera (U. Lyon 1)
# 2014 Lars Pastewka (U. Freiburg)
#
# 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
# i... | libAtoms/matscipy | scripts/fracture_mechanics/sinclair_plot.py | Python | lgpl-2.1 | 4,477 | [
"ASE",
"Matscipy"
] | 2889531412fd2b22d68fc48a77b2766f8417894a81557ed7cb7800e83b5e8dd3 |
#!/usr/bin/env python
'''
Author: Aditya Gilra, Jun 2016. (with inputs from Matthieu Gilson)
in Brian2rc3 for CAMP 2016.
'''
#import modules and functions to be used
from brian2 import * # importing brian also does:
# 'from pylab import *' which imports:
# matplot li... | h-mayorquin/camp_india_2016 | tutorials/LTPinnetworks2/Step1b_weight_distributions.py | Python | mit | 5,024 | [
"Brian",
"Gaussian",
"NEURON"
] | 8d930a3e3f0512e0218c1dae56d46f4f11dd9233c5e48de7d4c71bc156eaf9ae |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import numpy as np
from fractions import Fraction
from math import gcd, floor, cos
from functools import reduce
from pymatgen import Structure, Lattice
from pymatgen.core.sites import PeriodicSite
from monty.fr... | montoyjh/pymatgen | pymatgen/analysis/gb/grain.py | Python | mit | 117,726 | [
"CRYSTAL",
"pymatgen"
] | 325a0900d77417da4bd594b42bdf735510f0d1b896bc866251bf8ad04966df3b |
# -*- coding: utf-8 -*-
"""Collection of test signals which can be used to simulate dynamic measurements
and test methods.
This module contains the following functions:
* *shocklikeGaussian*: signal that resembles a shock excitation as a Gaussian
followed by a smaller Gaussian of opposite sign
* *GaussianPulse*: Ge... | eichstaedtPTB/PyDynamic | PyDynamic/misc/testsignals.py | Python | lgpl-3.0 | 7,837 | [
"Gaussian"
] | 1e5b2be210d75e4eeb83d0437ed13590b279b3fe6b736f036d57e354493c4de2 |
# 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 RAffyqcreport(RPackage):
"""QC Report Generation for affyBatch objects
This packag... | LLNL/spack | var/spack/repos/builtin/packages/r-affyqcreport/package.py | Python | lgpl-2.1 | 1,567 | [
"Bioconductor"
] | 5aacfccc89b0ee6bd234e2dd7c0961d514c73200cb8fab3c5886e92e903aad3d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
try:
from urllib.parse import urlsplit, urlparse, parse_qs, urljoin
except:
from urlparse import urlsplit, urlparse, parse_qs, urljoin
import re
import os
import requests
import time
import json
from base64 import b64decode
import copy
HTTP_HEADER = {
"User-Ag... | mrquim/repository.mrquim | repo/plugin.video.poseidon/resources/lib/modules/unshorten.py | Python | gpl-2.0 | 14,175 | [
"ADF"
] | 05eb340c497ca50359812ffb54bc4985036f9062975b9bac8cc1137ea1690f28 |
# -*- coding: utf-8 -*-
# Copyright (C) 2014 Canonical
#
# Authors:
# Galileo Sartor
#
# This program is free software; you can redistribute it and/or modify it under
# the terms of the GNU General Public License as published by the Free Software
# Foundation; version 3.
#
# This program is distributed in the hope tha... | LyzardKing/ubuntu-make | umake/frameworks/crystal.py | Python | gpl-3.0 | 3,312 | [
"CRYSTAL"
] | cff6d6f5ee616b59785b7f642444ec24f2be27f3b210885f905d684b897ad9a1 |
import ase
def extract_states_pdb(pdb_filename, x0_location, xN_location, x0_index, xN_index):
""" This function is an ASE wrapper that produces a start and end configuration from a PDB file containing multiple
conformation.
Args:
pdb_filename (str): The location of the PDB file.
x0_location (... | suttond/MODOI | SimulationUtilities/Extract_States_PDB.py | Python | lgpl-3.0 | 817 | [
"ASE"
] | 0468cde14e354e91e6e3d2c53ec25ba23c33ae7c76385857f4eee2f72070761b |
# pylint: disable=C0111
# pylint: disable=W0621
from lettuce import world, step
from lettuce.django import django_url
from common import TEST_COURSE_ORG, TEST_COURSE_NAME
@step('I register for the course "([^"]*)"$')
def i_register_for_the_course(_step, course):
cleaned_name = TEST_COURSE_NAME.replace(' ', '_')
... | abhinavp13/IITBX-edx-platform-dev | lms/djangoapps/courseware/features/registration.py | Python | agpl-3.0 | 1,553 | [
"VisIt"
] | 825ce77e3b970010e5a541e2a8671262db8f429978dfaf42da79f5188d007ebe |
# -*- coding: utf-8 -*-
'''The app module, containing the app factory function.'''
from flask import Flask, render_template
from octopus.settings import ProdConfig
from octopus.assets import assets
from octopus.extensions import (
bcrypt,
cache,
db,
login_manager,
migrate,
debug_toolbar,
nav,
misaka, p... | quaintm/octopus | octopus/app.py | Python | bsd-3-clause | 1,614 | [
"Octopus"
] | 05e3ddbd98c7df2acfb31c5e4f407d8433d5d6050d2c96944e11798d3de93722 |
#!/usr/bin/env python3
import os
import pathlib
from pathlib import Path
import numpy as np
from pysisyphus.helpers import geom_from_library, geom_from_xyz_file
from pysisyphus.calculators.Turbomole import Turbomole
THIS_DIR = pathlib.Path(os.path.dirname(os.path.realpath(__file__)))
def test_forces():
geom =... | eljost/pysisyphus | tests_staging/test_turbomole/test_turbomole.py | Python | gpl-3.0 | 1,544 | [
"TURBOMOLE"
] | c7f2f65582992bccaa1b200bed45b275815b9d6989d454560e404af88967e0be |
# -*- coding: utf-8 -*-
#
# Copyright 2008 - 2019 Brian R. D'Urso
#
# This file is part of Python Instrument Control System, also known as Pythics.
#
# Pythics 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, e... | dursobr/Pythics | pythics/proxies.py | Python | gpl-3.0 | 20,168 | [
"Brian"
] | 051a86263d2bf0a4d8b91ede2b1fabeb081b897314b8e95cbd678ef0aa5cbfc4 |
"""
Tests related to the cohorting feature.
"""
from uuid import uuid4
from common.test.acceptance.tests.discussion.helpers import BaseDiscussionMixin, BaseDiscussionTestCase
from common.test.acceptance.tests.discussion.helpers import CohortTestMixin
from common.test.acceptance.tests.helpers import UniqueCourseTest
fr... | synergeticsedx/deployment-wipro | common/test/acceptance/tests/discussion/test_cohorts.py | Python | agpl-3.0 | 5,802 | [
"VisIt"
] | 566a007a29175cb27f867934c0f1a320b2c01fe34b5ec3e1cf0de7fe044cc5f4 |
# python3
# pylint: disable=g-bad-file-header
# Copyright 2021 DeepMind Technologies Limited. 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... | deepmind/neural_testbed | neural_testbed/leaderboard/load.py | Python | apache-2.0 | 7,134 | [
"Gaussian"
] | 18e3849131509f25cf19baf50061134f72e12b4b0da41049322cc155aa8c5377 |
# -*- 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/topology/PQRParser.py | Python | gpl-2.0 | 7,252 | [
"Gromacs",
"MDAnalysis"
] | d77122644616617694a75891831e1280f9878b3fe33453bd06474a4716665151 |
############################ Copyrights and license ############################
# #
# Copyright 2012 Christopher Gilbert <christopher.john.gilbert@gmail.com> #
# Copyright 2012 Steve English <steve.english@navetas.com> ... | ahmad88me/PyGithub | github/Repository.py | Python | lgpl-3.0 | 155,573 | [
"Brian"
] | 08b5ff241440cfe706fef8cdf6fba66b27bdb4afc549c0de1f0289869e69f8c4 |
#!/usr/bin/env python
"""
Determine number of processors and memory for the worker node
"""
import multiprocessing
from DIRAC.Core.Base import Script
from DIRAC import gLogger, gConfig
from DIRAC.WorkloadManagementSystem.Utilities import JobParameters
__RCSID__ = "$Id$"
Script.setUsageMessage( '\n'.join( ['Get th... | Andrew-McNab-UK/DIRAC | WorkloadManagementSystem/scripts/dirac-wms-get-wn-parameters.py | Python | gpl-3.0 | 1,746 | [
"DIRAC"
] | 6d7a738c6fc4d3d3c46addc4fdb4d832a9700105b7a5b96ee74625c9edfbb9d4 |
# -*- coding: utf-8 -*-
#
# test_rate_neuron.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 Licens... | tobikausk/nest-simulator | pynest/nest/tests/test_rate_neuron.py | Python | gpl-2.0 | 4,910 | [
"NEURON"
] | 2f0ee503725fd44e40888d773e1811e1e934245285e8a1867a643a0a1860fa00 |
# 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/test/test_0006_water_pp_pb_nao.py | Python | apache-2.0 | 1,973 | [
"PySCF",
"SIESTA"
] | 57b9e1a37f89141fcf385363be3a66799406239e3952aad7d043f4bfde36c82e |
# /usr/bin/python
# Last Change: Sat Jun 09 10:00 PM 2007 J
# This is not meant to be used yet !!!! I am not sure how to integrate this
# stuff inside the package yet. The cases are:
# - we have a set of data, and we want to test online EM compared to normal
# EM
# - we do not have all the data before putting t... | jhmadhav/pynopticon | src/em/online_em.py | Python | gpl-3.0 | 14,078 | [
"Gaussian"
] | 26e072fe70623b322c3faa8714cfc99899d535fec07a62311616a4c9e3fec83e |
########################################################################
#
# (C) 2015, Brian Coca <bcoca@ansible.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation... | kisoku/ansible | lib/ansible/galaxy/__init__.py | Python | gpl-3.0 | 2,287 | [
"Brian",
"Galaxy"
] | 5c3f6f752d7bdee912d9e4116d9c946ad081678cbd560151c0b1e0c6ea6c3094 |
##
## This file is part of the libsigrokdecode project.
##
## Copyright (C) 2013 Uwe Hermann <uwe@hermann-uwe.de>
##
## 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 Li... | robacklin/sigrok | libsigrokdecode/decoders/midi/lists.py | Python | gpl-3.0 | 16,251 | [
"CRYSTAL"
] | 7eddcde90dc86d380e98e297ccee2cf65870be5262dce2871473cc894f173271 |
import numpy as np
from mayavi import mlab
from BDSpace.Figure.Sphere import Sphere
from BDSpace.Field import Field, SuperposedField
from BDSpace.Coordinates import transforms as gt
import BDSpaceVis as Visual
class ChargedBall(Field):
def __init__(self, q, r, name='Charged ball field', field_type='electrostat... | bond-anton/Space_visualization | demo/09_scalar_field.py | Python | apache-2.0 | 1,600 | [
"Mayavi"
] | 8321e8d9d0a889a87302f3b82d857e8570a0f650fc1296513dd083b54b20a9f8 |
from galaxy_analysis.plot.plot_styles import *
rc('font', size=22)#, ftype=42)
import yt
import numpy as np
from copy import copy
import sys
import deepdish as dd
from scipy.optimize import brentq
from galaxy_analysis.utilities import utilities
import h5py
from galaxy_analysis.utilities import functions
import matplo... | aemerick/galaxy_analysis | analysis/PDF.py | Python | mit | 37,448 | [
"Galaxy"
] | 01075cc71566a3ace4b4a08967149e80aec531095ba6fd35237924794f535925 |
##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-yapsa/package.py | Python | lgpl-2.1 | 2,814 | [
"Bioconductor"
] | 0f1036c70d3707c3f346a782097620a0319b42706ba7e128b66cb72989d91556 |
from django.utils import timezone
from dateutil.relativedelta import relativedelta
from edc_consent.models import ConsentType
from edc_registration.models import RegisteredSubject
from edc_constants.constants import (FAILED_ELIGIBILITY, OFF_STUDY, SCHEDULED, POS, YES,
NO, NEG, NOT_A... | TshepangRas/tshilo-dikotla | td_maternal/tests/test_maternal_ultrasound.py | Python | gpl-2.0 | 10,136 | [
"VisIt"
] | 1f44d15790b58ed9f00ebc17cdba6cc793c457bc4b956b2283ec3cbc50f3ebbe |
# Copyright 2008-2014 Nokia Solutions and Networks
#
# 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 l... | userzimmermann/robotframework-python3 | src/robot/result/testsuite.py | Python | apache-2.0 | 5,626 | [
"VisIt"
] | d3c3730726a2ca679c0e24deaf0856665b5bc6dd84d2035f3d0ce9c1bb95e1ce |
import numpy as np
from bayesnet.array.broadcast import broadcast_to
from bayesnet.linalg.cholesky import cholesky
from bayesnet.linalg.det import det
from bayesnet.linalg.logdet import logdet
from bayesnet.linalg.solve import solve
from bayesnet.math.exp import exp
from bayesnet.math.sqrt import sqrt
from bayesnet.ran... | ctgk/BayesianNetwork | bayesnet/random/multivariate_gaussian.py | Python | mit | 3,322 | [
"Gaussian"
] | 6bbdaedf8f4c3ba18e51cf90ffdf94a782b76e36f79fbc9f95c63de15b877c03 |
##
##
##
from basic import *
import util
import copy
import sys
from amino_acids import amino_acids
#import matplotlib
#if make_png: matplotlib.use('Agg')
#import matplotlib.pyplot as plt
#import numpy as np
with Parser(locals()) as p:
#p.str('args').unspecified_default().multiple().required()
p.str('organi... | phbradley/tcr-dist | file_converter.py | Python | mit | 14,446 | [
"BLAST"
] | 92da1f0d0e6e2e3d19ca4cc31e85428027383365efa76179b63a3e7f8e26179a |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/view/controls/editors/imageeditor.py | Python | gpl-2.0 | 9,076 | [
"VisIt"
] | ba14d8c56a9a183c62dd5d8ca43e65aac3d179d6c52e111ce5efca0331237814 |
from Bio import ExPASy
from Bio import SeqIO
from collections import Counter
import numpy as np
import matplotlib.pyplot as plt
import csv
from matplotlib.backends.backend_pdf import PdfPages
AA_LETTERS = sorted("ACEDGFIHKMLNQPSRTWVY")
# list all proteins in ecoli by uniprot_ID - aprse from .txt file
UPID_list = []
... | eladnoor/proteomaps | src/collapse_not_mapped.py | Python | mit | 3,335 | [
"Biopython"
] | 7c05e26856d0ce00cbec6bd67d95b1fd7636abbcfd90f2af4464169fce8409de |
#this script is do Gaussian modeling for multiple minerals and output the paramters like DT's method.
import spectral.io.envi as envi
import ModifiedGaussianModel as MGM
import numpy as np
import pre_processing_mineral as ppm
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
import pandas as p... | Vincentyao1995/Globalink2017-UBC | Vincent/REE_Patterns/Experiment8.py | Python | mit | 11,553 | [
"Gaussian"
] | 07bd44501d92f862def6589d9af68f39a1e0b0d2c2ec83418f7fbb92fa6b15f8 |
#!/usr/bin/env python
# -*- coding: UTF-8 -*-
"""
SAM alignment format. There are other tools that handles better SAM and BAM.
This script simply parses the lines in SAM into human readable fields.
http://samtools.sourceforge.net/SAM1.pdf
"""
import os
import os.path as op
import sys
import logging
from collections... | orionzhou/robin | formats/sam2.py | Python | gpl-2.0 | 29,667 | [
"Bowtie",
"HTSeq",
"pysam"
] | cb86ea10844469f99b953fefb0214597bf036911df2ea20a0fbee30bd2ba2ac5 |
#!/usr/bin/env python
#
# Copyright (c) 2000 Autonomous Zone Industries
# This file is licensed under the
# GNU Lesser General Public License v2.1.
# See the file COPYING or visit http://www.gnu.org/ for details.
#
__cvsid = '$Id: UnreliableHandicapper.py,v 1.2 2002/02/11 14:47:57 zooko Exp $'
# standard modul... | zooko/egtp | common/UnreliableHandicapper.py | Python | agpl-3.0 | 1,705 | [
"VisIt"
] | 32f5d1485c7c55e13c536328bd536233ffb9c4338d83b6d5bdd9a7380d25b5b6 |
#!/usr/bin/env python3
import numpy as np
class Activator:
"""Contains Activation functions for NeuralNet.
Currently contains implementations of sigmoid, tanh, elu,
and softmax functions
"""
@staticmethod
def sigmoid(signal, deriv=False):
"""Sigmoid Activation.
Args:
... | ZahidDev/NeuralNet | NeuralNet/activations.py | Python | mit | 3,145 | [
"NEURON"
] | 5b3f10e3b362c9bc52f61f4f39162c1afb6af7c6916750280cd33949465e6d49 |
#!/usr/bin/env python2
desc="""Report coverage from BAM file.
Support spliced alignments and mapping quality filtering.
By default ignores secondary alignments, duplicates and quality failed reads.
Dependencies:
- pysam (sudo easy_install -U pysam)
TDB:
- define minimum overlap
"""
epilog="""Author: l.p.pryszcz+git... | lpryszcz/bin | bam2cov_multi_pool.py | Python | gpl-3.0 | 8,980 | [
"pysam"
] | 927ba2b5f310755f30e5425e064e88d411efc3c64132a10d3afced6253ecd5bd |
"""
Algorithms for imputing missing values in data
"""
import numpy as np
try:
import sklearn
except ImportError:
sklearn = False
else:
from sklearn.cross_decomposition import PLSRegression
def gaussian(df, width=0.3, downshift=-1.8, prefix=None):
"""
Impute missing values by drawing from a norma... | mfitzp/padua | padua/imputation.py | Python | bsd-2-clause | 3,229 | [
"Gaussian"
] | 9f2db414157d3594fc195584cb193d706b2f729160807d40621bc7568c4f22f1 |
__date__ = '5/29/14'
__author__ = 'ABREZNIC'
import os, arcpy, xlwt, datetime, math, multiprocessing, shutil, smtplib, base64, sys
# date
now = datetime.datetime.now()
curMonth = now.strftime("%m")
curDay = now.strftime("%d")
curYear = now.strftime("%Y")
today = curYear + "_" + curMonth + "_" + curDay
runday = now.st... | adambreznicky/python | QC/pre_GRID/ErrorChecks_v3.py | Python | mit | 108,094 | [
"VisIt"
] | a9007aa05cf5a8fd128a04daf410b5c1d69102c43f2128928a68cb1678c20a10 |
from django.core.urlresolvers import reverse
from django.http import HttpResponseRedirect
from django.utils.translation import ugettext_noop, ugettext as _
from djangular.views.mixins import JSONResponseMixin, allow_remote_invocation
from corehq import privileges
from corehq.apps.app_manager.dbaccessors import domain_... | qedsoftware/commcare-hq | corehq/apps/dashboard/views.py | Python | bsd-3-clause | 10,306 | [
"VisIt"
] | 1b3606b49c0b27a9f5a422d4fa52dc1de0f7ab3a46f73b154b2d25870a15d3a8 |
"""
A bunch of random examples in no apparent order. However, almost every feature
is demonstrated here.
"""
from py2scad import *
import scipy
if 0:
c = Circle(r=2.0)
s = Square(size=[3,1])
p = Polygon(points=[[0,0],[1,0],[1,1]], paths=[[0,1,2]])
p.write('test.scad',fn=100)
print p
print c
i... | acrobotic/py2scad | examples/smorgasbord.py | Python | apache-2.0 | 5,742 | [
"Gaussian"
] | ea4476ae4007c24a601705c9b3bdfc883ee9fa976dee6cd219ba040acae9e5f9 |
# coding=utf-8
# Copyright 2022 The Google Research Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicab... | google-research/google-research | xirl/sac/agent.py | Python | apache-2.0 | 9,311 | [
"Gaussian"
] | e347eb4ad5ef712f6780063e024a275398c241441476510528911662908302d8 |
#!/usr/bin/python
"""
Copyright 2015 Paul Willworth <ioscode@gmail.com>
This file is part of Galaxy Harvester.
Galaxy Harvester 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 th... | druss316/G-Harvestor | html/getFeedback.py | Python | gpl-3.0 | 7,031 | [
"Galaxy"
] | e29e9c43ae89e79f173dc8cfc96e097e2193b031f5c9072098923941e6dcc547 |
# -*- coding: utf-8 -*-
#
# enaml-native documentation build configuration file, created by
# sphinx-quickstart on Sat Feb 24 14:59:48 2018.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# autogenerated file.
... | codelv/enaml-native | docs/conf.py | Python | mit | 12,136 | [
"Amber"
] | 637e8d66189a6caf5e9e665f67d940acb538c4ae021756ef829f017fd875cab1 |
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