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# Hidden Markov Models
#
# Author: Ron Weiss <ronweiss@gmail.com>
# and Shiqiao Du <lucidfrontier.45@gmail.com>
# API changes: Jaques Grobler <jaquesgrobler@gmail.com>
# Modifications to create of the HMMLearn module: Gael Varoquaux
"""
The :mod:`hmmlearn.hmm` module implements hidden Markov models.
"""
import string... | mvictor212/hmmlearn | hmmlearn/hmm.py | Python | bsd-3-clause | 86,425 | [
"Gaussian"
] | 19a4450581a99821191d53a76876daacd8743215246d11e2a20ba9cf38c1316a |
# Copyright 2013-2021 The Meson development team
# 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 agree... | jpakkane/meson | mesonbuild/dependencies/detect.py | Python | apache-2.0 | 9,556 | [
"NetCDF"
] | e5d422289eb4812f326d7abfd143c321aaf2c1206e74a5339751b811aaed5d25 |
"""
Django settings for octopus project.
Generated by 'django-admin startproject' using Django 1.8.2.
For more information on this file, see
https://docs.djangoproject.com/en/1.8/topics/settings/
For the full list of settings and their values, see
https://docs.djangoproject.com/en/1.8/ref/settings/
"""
# Build path... | gregorianzhang/octopus | octopus/settings.py | Python | apache-2.0 | 2,882 | [
"Octopus"
] | 046ac1f1f3d658fe0012fd5849070e6523bb1c26187fbec0a4d2410cf498133c |
#!/usr/bin/env ipython
from pylab import *
import numpy as np
from scipy.io.netcdf import netcdf_file
import console_colors as ccl
import os
MCwant = '2'
nbefore = 2
nafter = 4
WangFlag = '90.0' #'NaN'
fgap = 0.2
#v_lo = 550.0 #550.0 #450.0 #100.0
#v_hi = 3000.0 #3000.0 #550.0 #... | jimsrc/seatos | sheaths/src/surf.dens_for.paper/src/h_group_Bmc.py | Python | mit | 3,805 | [
"NetCDF"
] | 3a26bdd015a835de49101f44bf009ea6a4333547735e80f626d7027b39fcb3f7 |
import numpy as np
from scipy.optimize import fsolve
from astropy.utils import isiterable
def stellarmass_from_halomass(log_Mhalo, z=0):
""" Stellar mass from Halo Mass from Moster+2013
https://doi.org/10.1093/mnras/sts261
Args:
log_Mhalo (float): log_10 halo mass
in solar mass units.... | FRBs/FRB | frb/halos/utils.py | Python | bsd-3-clause | 1,986 | [
"Galaxy"
] | d130a8fea954015b8d4ba26c652fee4eb14dd98f1af00fcc1cc21643e649ea56 |
# Nucleotide analysis from VCF files
# (c) 2017 Ali Rassolie
# Lumina sequencing
class annuc:
def __init__(self, **kwargs):
# Imports
# Kwarg handling
self.spec_input = kwargs["dictinput"]
self.hass_input = kwargs["hass"]
self.output = "{}_" #kwargs["output"]
self.searchtype = kwargs["sear... | HypoChloremic/annuc | annuc_v2.py | Python | mit | 4,410 | [
"BWA"
] | 38be610dea149d157172123199b0caad6efc8254f437166cfa1324cd2441ec16 |
# $Id$
#
# Copyright (c) 2013, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
# 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 retain the above c... | adalke/rdkit | rdkit/Chem/Draw/SimilarityMaps.py | Python | bsd-3-clause | 14,928 | [
"RDKit"
] | e501b16fb34fa4a607cc68a45927629541e69824af160ade61ced5a31e0a8485 |
##############################################################################
# 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-statmod/package.py | Python | lgpl-2.1 | 2,037 | [
"Gaussian"
] | affc16ba8eba9395bc9c09802209a659873b1e1e8a44dc1f6e9198923ca2a789 |
import logging, tempfile
from time import time, gmtime, strftime
from DIRAC.Core.Utilities import Time
from dirac.lib.base import *
from dirac.lib.diset import getRPCClient
from dirac.lib.credentials import authorizeAction
from DIRAC import gConfig, gLogger
from DIRAC.Core.Utilities.DictCache import DictCache
import ... | DIRACGrid/DIRACWeb | dirac/controllers/jobs/SiteGateway.py | Python | gpl-3.0 | 19,138 | [
"DIRAC"
] | 60e11f6acde89255ca0808b40d8da0d0f2c02240ca120282fafd15099cac7d5b |
'''plotChromVariantFrequency.py
Usage:
plotChromVariantFrequency.py <mincov> <outfile> <snpfiles>...
'''
import collections
import os
import re
import pysam
import matplotlib as mpl
mpl.use('Agg')
import matplotlib.pyplot as plt
from general_python import docopt
import numpy as np
# Extract and process argume... | adam-rabinowitz/ngs_python | scripts/Variants/plotVariantFrequency.py | Python | gpl-2.0 | 3,550 | [
"pysam"
] | 1b257488f0b93da7fd8428f27b455f8b754f083823b53e59f2417e0bdbcefeb0 |
# (c) 2013-2014, Michael DeHaan <michael.dehaan@gmail.com>
# (c) 2015 Toshio Kuratomi <tkuratomi@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, either... | brandond/ansible | lib/ansible/executor/module_common.py | Python | gpl-3.0 | 42,417 | [
"VisIt"
] | 2717c6e8dec60d4b5e2abcae29cf985dc75f565f276fcf39ee3623043cb46f53 |
"""
Tests on the models
"""
from octopus.modules.es.testindex import ESTestCase
from service import models
from service.tests import fixtures
from octopus.lib import dataobj, dates
import time
class TestModels(ESTestCase):
def setUp(self):
super(TestModels, self).setUp()
def tearDown(self):
s... | JiscPER/jper-sword-out | service/tests/unit/test_models.py | Python | apache-2.0 | 4,823 | [
"Octopus"
] | 2f55e53640fb8cd32a18e7996fce42bb312fedb6ed1ad3c79f41d91b5ab23163 |
import base64
import json
import re
import string
import sys
import unicodedata
import time
import BaseHTTPServer
import SocketServer
from urlparse import urlparse
from rauth import OAuth1Service, OAuth2Service
rdio_client_id=''
rdio_client_secret=''
spotify_client_id=''
spotify_client_secret=''
page_size = 50
redire... | streeter/Rdio2Spotify | main.py | Python | mit | 18,693 | [
"VisIt"
] | 4a2cb927cb652c84135f8ef97b383e3ff7db1df58615275c5f014f3e77d5082c |
# encoding: utf-8
import os
import argparse
import sys
import re
import pytest
from txtemplates import server_templates
import txtemplates
def test_get_parser_error(capsys):
parser = server_templates.get_parser()
with pytest.raises(SystemExit):
parser.parse_args([])
_, err = capsys.readouterr()
... | mdrohmann/txtemplates | tests/server_templates/test_server_templates.py | Python | bsd-3-clause | 3,487 | [
"VisIt"
] | fd9ced3a2ee12e707af6c562ca4fdc30006f33959c066a306820738104afb8f2 |
################################################################################
# Peach - Computational Intelligence for Python
# Jose Alexandre Nalon
#
# This file: tutorial/xor-problem.py
# Solving the exclusive-or problem
################################################################################
# Please, fo... | anki1909/peach | tutorial/neural-networks/xor-problem.py | Python | lgpl-2.1 | 1,332 | [
"NEURON"
] | dfbcdd81da8c95e7259d95b2a11aa13beaabe42055c6cf4ed06d5b19d2eeb223 |
#!/usr/bin/env python
#
# Electrum - Lightweight Bitcoin Client
# Copyright (C) 2015 Thomas Voegtlin
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
# (the "Software"), to deal in the Software without restriction,
# including without... | neocogent/electrum | electrum/plugins/trustedcoin/qt.py | Python | mit | 13,106 | [
"VisIt"
] | f2e53cc16162d43d4fe1378acbac7fc1d8d16a79a35fe7799f1a2136c998647c |
# (c) 2012-2018, Ansible by Red Hat
#
# This file is part of Ansible Galaxy
#
# Ansible Galaxy is free software: you can redistribute it and/or modify
# it under the terms of the Apache License as published by
# the Apache Software Foundation, either version 2 of the License, or
# (at your option) any later version.
#
... | chouseknecht/galaxy | galaxy/settings/production.py | Python | apache-2.0 | 6,084 | [
"Galaxy"
] | 5cecc693530d5ccf5f5b75affe9c9f41a4666908e2dec9ecdda777524b92287b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Running the tests:
# $ python3 -m unittest discover --start-directory ./tests/
# Checking the coverage of the tests:
# $ coverage run --include=./*.py --omit=tests/* -m unittest discover && rm -rf ../html_dev/coverage && coverage html --directory=../html_dev/coverage --t... | e2jk/vallenato.fr | bin/tests/test_youtube.py | Python | agpl-3.0 | 2,489 | [
"VisIt"
] | 5a0bdce9f7447e51786432a2d39bcea0b298ec97a8c80355e353cbc12305d0db |
##############################################################################
# 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-affypdnn/package.py | Python | lgpl-2.1 | 1,740 | [
"Bioconductor"
] | 9881aa7eb524afec694c186c7a03f9d65b554ba6c2b4f9d433aa84219e13e081 |
# Copyright (c) 2012 Google Inc. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
from __future__ import with_statement
import collections
import errno
import filecmp
import os.path
import re
import tempfile
import sys
# A minimal memoizing d... | dreamllq/node | tools/gyp/pylib/gyp/common.py | Python | apache-2.0 | 20,003 | [
"VisIt"
] | ee3bc8926856c9a8e4e408923a4656c831225c519b5001d1471f558b72220166 |
import numpy as np
def affine_forward(x, w, b):
"""
Computes the forward pass for an affine (fully-connected) layer.
The input x has shape (N, d_1, ..., d_k) and contains a minibatch of N
examples, where each example x[i] has shape (d_1, ..., d_k). We will
reshape each input into a vector of dimension D = ... | arasdar/DL | stanford-cs231n-master/assignment2/layers.py | Python | unlicense | 24,727 | [
"NEURON"
] | 21848bb54fb7390e5b848502fa1e66f8c248383560e5752e88acfd3dd0a51752 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# vim:fenc=utf-8
#
# Copyright © 2017 Malcolm Ramsay <malramsay64@gmail.com>
#
# Distributed under terms of the MIT license.
"""Compute dynamic properties."""
import logging
from typing import Any, Dict
import numpy as np
import pandas
from scipy.stats import spearmanr
... | malramsay64/MD-Molecules-Hoomd | statdyn/analysis/dynamics.py | Python | mit | 18,128 | [
"Gaussian"
] | 77f0b49ff3a0260e1cdd1abc789f0e00d86bd81e9db711794b71c09bed72bf85 |
import os
import sys
import functools
import collections
import scandir
PY2 = sys.version_info.major == 2
PY3 = sys.version_info.major == 3
if PY3:
basestring = str
unicode = str
if PY2:
unicode = unicode
basestring = basestring
def fnwalk(path, fn, shallow=False):
"""
Walk directory tree... | Outernet-Project/fsal | fsal/utils.py | Python | gpl-3.0 | 4,673 | [
"VisIt"
] | 0501e44d24e22755076cd3b23ac27e5072bd3c542728b476c1615e2ad25c8949 |
#!/usr/bin/env python
# Copyright (C) 2013,2014 The ESPResSo project
# Copyright (C) 2012 Olaf Lenz
#
# 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 versio... | mkuron/espresso | src/config/gen_sampleconfig.py | Python | gpl-3.0 | 1,891 | [
"ESPResSo"
] | b3c0eed0fe79541e1b9a7e92945d7505284e1acf7b6dd1755bf621667f0961f5 |
#!/usr/bin/env
"""
NARRuv_quiver_plot.py
"""
#System Stack
import datetime, sys
#Science Stack
from netCDF4 import MFDataset, num2date
import numpy as np
# Visual Stack
import matplotlib as mpl
import matplotlib.pyplot as plt
from matplotlib.dates import MonthLocator, DateFormatter
import matplotlib.ticker as tic... | shaunwbell/FOCI_Analysis | general_plotting_routines/cftime_uv_quiver_plot.py | Python | mit | 4,936 | [
"NetCDF"
] | 95cbd9d3f32602f799e1b99c3fb8ed6dea5ef9e40324743cfb800ebe3eaae57e |
# -*- coding: utf-8 -*-
from django.conf import settings
GATEWAY_HOST = "www.moneybookers.com"
GATEWAY_URI = "/app/payment.pl"
TEST_GATEWAY_URI = "/app/test_payment.pl"
GATEWAY = "https://%s%s" % (GATEWAY_HOST, GATEWAY_URI)
TEST_GATEWAY = "https://%s%s" % (GATEWAY_HOST, TEST_GATEWAY_URI)
MERCHANT_ID = settings.MONEYB... | mikery/django-moneybookers | moneybookers/conf.py | Python | bsd-2-clause | 14,814 | [
"BWA"
] | bf437c042d5dbf23114bf0cff4b9de08b486310961afb9814e43b7843f325410 |
"""
Extended math utilities.
"""
# Authors: Gael Varoquaux
# Alexandre Gramfort
# Alexandre T. Passos
# Olivier Grisel
# Lars Buitinck
# Stefan van der Walt
# Kyle Kastner
# License: BSD 3 clause
from __future__ import division
from functools import partial
import ... | ashhher3/scikit-learn | sklearn/utils/extmath.py | Python | bsd-3-clause | 20,800 | [
"Gaussian"
] | ca307aabe8b8079b78003816c9b5c5d1567c86343f6a89687f1ea35898e66187 |
# Author: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Copyright (c) 2009, Enthought, Inc.
# License: BSD Style.
import numpy as np
from scipy import special
from mayavi import mlab
##############################################################################
# Function to caculate the Magnetic field generated... | arakcheev/python-data-plotter | magnetic_example.py | Python | mit | 7,716 | [
"Mayavi"
] | 52622903629e2736fbbffe93c5f85276b72c7deb93aaf179a65db5b39ab0b1a6 |
# ----------------------------------------------------------------------
# Numenta Platform for Intelligent Computing (NuPIC)
# Copyright (C) 2020, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This progra... | numenta/nupic.research | packages/backprop_structure/src/nupic/research/frameworks/backprop_structure/modules/vdrop_layers.py | Python | agpl-3.0 | 26,779 | [
"Gaussian"
] | a0db6a02e14aad3da0459f55c35938a0b7a49704cbc5b273781649587604bdad |
#! /usr/bin/env python
import sys
import numpy as np
import ase
from ase.io import read, write
from ase.optimize import FIRE
from ase.md import Langevin
from ase.units import mol, fs, kB
from atomistica.logger import MDLogger
from liquid_tools import *
###
# For coordination counting
#densitie... | Atomistica/atomistica | examples/ASE/quench.py | Python | gpl-2.0 | 4,125 | [
"ASE"
] | 9a717881f33d2126d999a31864986ec00b752146c0574243104e05992430bd9c |
"""
tests for Quicklook QA class and functions. It also indludes tests on low level functions on desispec.qa.qalib
"""
import unittest
import shutil
import tempfile
import numpy as np
import os
from desispec.qa import qalib
from desispec.qa import qa_quicklook as QA
from pkg_resources import resource_filename
import d... | desihub/desispec | py/desispec/test/test_ql_qa.py | Python | bsd-3-clause | 21,707 | [
"Gaussian"
] | 03aa510a0110c45a4ed62588477d30f506e463319d987813457afd108b72d6d8 |
from __future__ import print_function, unicode_literals
from builtins import zip
from builtins import range
import sys
import re
import warnings
import itertools
import string
import math
import numpy as np
import Bio.PDB as bpdb
from collections import defaultdict
import forgi.utilities.debug as fud
import forgi.thr... | ViennaRNA/forgi | forgi/threedee/utilities/pdb.py | Python | gpl-3.0 | 41,262 | [
"Biopython"
] | d21d43aa735112374187fa8bebf45c08b464a6b8b7f82208f1f74374b1869d1d |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# scripts - backend to generate user and resource scripts
# Copyright (C) 2003-2015 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gen... | heromod/migrid | mig/shared/functionality/scripts.py | Python | gpl-2.0 | 12,310 | [
"Brian"
] | cfa847d46cc516e87af81b95dea615a896e2d1286cdd44786e524f4fcb63de63 |
# -*- 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,
... | ProgressivePlanning/mongoengine | tests/document/instance.py | Python | mit | 102,382 | [
"exciting"
] | 59112097f7b169429819c95c7da201addee28d132eeca4245713a7463c4681d8 |
# Copyright (C) 2011 by Brandon Invergo (b.invergo@gmail.com)
# 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
import os
import os.path
from ._paml import Paml, _... | zjuchenyuan/BioWeb | Lib/Bio/Phylo/PAML/codeml.py | Python | mit | 9,172 | [
"Biopython"
] | f12a087bc6a98a90a8ce91a82c8f1db98354c6b49fed80bb02d5e84f6234f585 |
from aces.materials import Material
from aces.modify import get_unique_atoms
from ase import Atoms,Atom
from math import pi,sqrt
from ase.dft.kpoints import ibz_points
from ase.lattice import bulk
from ase import io
from aces import config
from aces.tools import *
class structure(Material):
def set_parameters(self):
... | vanceeasleaf/aces | aces/materials/CoSb3.py | Python | gpl-2.0 | 2,865 | [
"ASE"
] | 6fd9f47211bf8a8019f5fd11e21a3456b91695ef605b1d3e30c448d26e208900 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2007 Zsolt Foldvari
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2009 Brian Matherly
# Copyright (C) 2010 Peter Landgren
# Copyright (C) 2010 Jakim Friant
# Copyright ... | arunkgupta/gramps | gramps/plugins/lib/libcairodoc.py | Python | gpl-2.0 | 60,637 | [
"Brian"
] | 7546da03fa7585d5c02a83a89e09b3cd4dd7b8afe2fa835094bf2bc460d37ad9 |
import os, re
import argparse
import pandas as pd
parser = argparse.ArgumentParser(description='Pars GASSST to blast output')
parser.add_argument('-i', type=str,dest='input',
help='Input GASSST output File')
parser.add_argument('-o', dest='Output', type=str,default=os.path.join(os.getcwd(),"out.t... | bioinfo-core-BGU/neatseq-flow_modules | neatseq_flow_modules/Liron/Gassst_module/Gassst2blast.py | Python | gpl-3.0 | 1,841 | [
"BLAST"
] | 92b04623853ec65f4b17e9c7854a5bb08e05cab1d8b51794e63441e713455dab |
"""Plotting functions for visualizing distributions."""
from __future__ import division
import numpy as np
from scipy import stats
import pandas as pd
import matplotlib as mpl
import matplotlib.pyplot as plt
import warnings
from six import string_types
try:
import statsmodels.nonparametric.api as smnp
_has_st... | JWarmenhoven/seaborn | seaborn/distributions.py | Python | bsd-3-clause | 28,496 | [
"Gaussian"
] | 107182888b8b61637a46f711ec8d4cfa138b12d5b45970dadc5f22afddc8be24 |
# -*- coding: utf-8 -*-
"""
This module contains a custom streamlining class derived from the MayaVi2
streamlining class, modified to accept an array of seed points for visulaisation
using mayavi.
.. warning::
The documentation for this class cannot be built on Read The Docs, it is possible to build it locally.
Y... | Alex-Ian-Hamilton/solarbextrapolation | solarbextrapolation/mayavi_seed_streamlines.py | Python | mit | 4,775 | [
"Mayavi"
] | 9f9f7d488baa6601ce2be2669dda93c50c37ddd7a7e06a945651aab794fd4610 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""Downloads poems from poets.org and saves them to a text file.
This is just a quick hack, but it's licensed under the GNU GPL, either version
3 or, at your option, any later version; see the file LICENSE.md for details.
This code is copyright 2017 by Patrick Mooney.
""... | patrick-brian-mooney/LibidoMechanica | scrapers/poets.org.py | Python | gpl-3.0 | 3,025 | [
"Brian"
] | 1841d6cb14694226e59e52f5c75271eafb1bc78851213b517cab9220dd39d0a1 |
#!/usr/bin/env python
##############################################################################################
#
#
# 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://www.ukca.ac.u... | acsis-project/emissions | emissions/python/timeseries_1960-2020/regrid_HCHO_emissions_n96e_360d.py | Python | gpl-3.0 | 17,334 | [
"NetCDF"
] | fd2e578bd49485db8ae7cf8cbd6d01c3b012f751a20559d0d3822cd25d8e078b |
import os
from ase import *
from ase.parallel import rank, barrier
from gpaw.utilities import equal
from gpaw import Calculator
from gpaw.atom.generator import Generator
from gpaw.atom.configurations import parameters
from gpaw.xc_functional import XCFunctional
from gpaw import setup_paths
def test():
# Generate s... | qsnake/gpaw | oldtest/nonselfconsistentvdw.py | Python | gpl-3.0 | 878 | [
"ASE",
"GPAW"
] | 14f12a39de28264ccac2a0340a79b760a0642bf236fd62535d03a1faffec17e6 |
"""
Methods related to importing data.
"""
import copy
import csv
import os
import shutil
import re
import subprocess
from tempfile import mkdtemp
from tempfile import mkstemp
from tempfile import NamedTemporaryFile
from BCBio import GFF
from Bio import Entrez
from Bio import SeqIO
from celery import task
from django... | woodymit/millstone_accidental_source | genome_designer/utils/import_util.py | Python | mit | 38,681 | [
"BWA",
"Biopython"
] | 002d0d358747e9442302be2f0dd42edc954275595558828bed8a84ea1eb5c930 |
from aiida import load_dbenv
load_dbenv()
from aiida.orm import Code, DataFactory, WorkflowFactory
StructureData = DataFactory('structure')
ParameterData = DataFactory('parameter')
import numpy as np
# Silicon structure
a = 5.404
cell = [[a, 0, 0],
[0, a, 0],
[0, 0, a]]
symbols=['Si'] * 8
scaled_pos... | abelcarreras/aiida_extensions | workflows/launcher/launch_gruneisen_lammps_si.py | Python | mit | 3,040 | [
"LAMMPS",
"phonopy"
] | 77ae717e70d8f2b30df4add5269fbc9e596eaf7e012704851680b895b595fdda |
import dryscrape
# make sure you have xvfb installed
dryscrape.start_xvfb()
search_term = 'dryscrape'
# set up a web scraping session
sess = dryscrape.Session(base_url = 'http://google.com')
# we don't need images
sess.set_attribute('auto_load_images', False)
# visit homepage and search for a term
sess.visit('/')
... | carlosb1/examples-python | ideas/mango-example/google.py | Python | gpl-2.0 | 581 | [
"VisIt"
] | 9e03133d3a5006d142381ee228a87c959ee48a4edf20e4729c1fe65718dca07b |
# -*- coding: utf-8 -*-
from django.http import HttpRequest, HttpResponse, HttpResponseForbidden, HttpResponseRedirect
from salesReport.pymagento import Magento
import csv, math
from datetime import date, timedelta, datetime
import models
from django.shortcuts import render_to_response
from django.template import Reque... | akiokio/centralfitestoque | src/salesReport/views.py | Python | bsd-2-clause | 36,745 | [
"VMD"
] | 72d5a25c76f846018f6a30ddb98d129a87a2374d3e7f551bd85d7e9a6a81d92f |
# -*- coding: utf-8 -*-
#
# This file is part of INSPIRE.
# Copyright (C) 2014-2017 CERN.
#
# INSPIRE 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 ... | chris-asl/inspire-query-parser | inspire_query_parser/ast.py | Python | gpl-3.0 | 4,970 | [
"VisIt"
] | 81960f74b7ecb8c212fb93781267188b691f37831d26f8bead2f603535554759 |
# Copyright 2013 by David Arenillas and Anthony Mathelier. 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.
"""Provides read access to a JASPAR5 formatted database.
This modules re... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/motifs/jaspar/db.py | Python | apache-2.0 | 27,398 | [
"Biopython"
] | 48e9be23d31878e210b8e45c96d3110b728e53f5092e017e9e5fde00a9d31272 |
"""
From the 26 March meeting, the plan was:
1) Fix 2D separation and overall R flux ratio. Find best fit PSF.
Issues... the best fit PSF can't just be a Gaussian. It is naturally the convolution of
multiple functional forms, i.e. something that is positive everywhere. On a quick search,
I can't find any obvious para... | PyWiFeS/tools | spectroastro2D.py | Python | mit | 4,907 | [
"Gaussian"
] | 63a08e37e02e74f02b6b9dd722f57f93138270ea11f06f045bdafcde5b968a7b |
"""
Mixture models for multi-dimensional data.
Reference: Hirsch M, Habeck M. - Bioinformatics. 2008 Oct 1;24(19):2184-92
"""
import numpy
from abc import ABCMeta, abstractmethod
class GaussianMixture(object):
"""
Gaussian mixture model for multi-dimensional data.
"""
_axis = None
# prior for v... | csb-toolbox/CSB | csb/statistics/mixtures.py | Python | mit | 13,837 | [
"Gaussian"
] | 08e23ea1b083aaa5dc13720731d332cd4a8e21350aa4d35f95d15bccf04ef67f |
#!/usr/bin/python
# Copyright: (c) 2017, Ansible Project
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
'status': ['st... | ppanczyk/ansible | lib/ansible/modules/files/xattr.py | Python | gpl-3.0 | 6,151 | [
"Brian"
] | 2866466edd58488e58f0e604b2f8014fbc557c54c1991ce601f9a5816a828553 |
import numpy as np
import numba as nb
from PolyLibScan.Analysis.sim_run import AtomFilter
def distance_to_active_site(xyz_coords, db, polymer_ids, active_site_no):
'''calculates the minimal distance between the polymer and the
active site.
'''
type_filter = AtomFilter(db.traj_type_order, db.sequenc... | luminescence/PolyLibScan | Save/compute.py | Python | mit | 941 | [
"LAMMPS"
] | 7a2675683cd0dc23a6e3d1898d153956efda967d7430fd457ce7698654af3394 |
# Copyright (c) 2010-2014 Bo Lin
# Copyright (c) 2010-2014 Yanhong Annie Liu
# Copyright (c) 2010-2014 Stony Brook University
# Copyright (c) 2010-2014 The Research Foundation of SUNY
#
# Permission is hereby granted, free of charge, to any person
# obtaining a copy of this software and associated documentation files
#... | mayli/DistAlgo | da/compiler/parser.py | Python | mit | 75,023 | [
"VisIt"
] | 57856c58d63832945ade8936a3106007f0b2172db46e51cd8343f8729fe7bd4b |
###############################################################################
# Settings file for birdie stress tests
###############################################################################
# base URL of installation
BASE_URL='http://localhost:6543'
DB_FILE='sqlite:///fakeusers.sqlite'
# pre-registered use... | simonwoo/Birdie_Redis | birdie-stress/test_scripts/birdie_settings.py | Python | mit | 1,619 | [
"VisIt"
] | 3070101d5bd4378cca14a1433d63418146b2400696440c153506760fb6400dbb |
import calendar
import json
import re
import uuid
import mock
from django.core.cache import cache
from django.contrib.auth.models import User
from django.core import mail
from django.core.urlresolvers import reverse
from nose.tools import eq_, ok_
from airmozilla.main.models import Event
from airmozilla.base.tests.... | kenrick95/airmozilla | airmozilla/comments/tests/test_views.py | Python | bsd-3-clause | 21,315 | [
"VisIt"
] | e6667e7c63b2ef59a810ebb389617d2e404b7a9073fe86b9b431ba12a26b8dad |
#!/usr/bin/env python
# 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
#
# U... | gkc1000/pyscf | pyscf/df/r_incore.py | Python | apache-2.0 | 3,656 | [
"PySCF"
] | 34d74dfb2f8e5f20eb8eb61b21c2e9e3cf87b1dbc2eab52c8a3330c759188dac |
"""Script to list all the modules and packages used by a Brython page
It parses the HTML page, detecting the tags <script type="text/python"> and
gets the Python code embedded inside these tags, or of the external Python
scripts if the tag has an attribute "src".
Use module ast to detect all the imports in the script... | jonathanverner/brython | scripts/find_modules.py | Python | bsd-3-clause | 10,215 | [
"VisIt"
] | 9dec1b6788b3c234315dd575984e4ca6feccd6330b7a4e685797d8ffd23bc938 |
# coding=utf-8
# Copyright 2022 Google LLC.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed ... | tensorflow/model-remediation | tensorflow_model_remediation/min_diff/losses/kernels/gaussian_kernel.py | Python | apache-2.0 | 2,796 | [
"Gaussian"
] | 9c2479f693c761a2da7bf9aabfb1a19ee60b0c5d42389212501774c8f053356a |
"""
This module gathers tree-based methods, including decision, regression and
randomized trees. Single and multi-output problems are both handled.
"""
# Authors: Gilles Louppe <g.louppe@gmail.com>
# Peter Prettenhofer <peter.prettenhofer@gmail.com>
# Brian Holt <bdholt1@gmail.com>
# Noel Da... | chaluemwut/fbserver | venv/lib/python2.7/site-packages/sklearn/tree/tree.py | Python | apache-2.0 | 31,383 | [
"Brian"
] | c857f8eaf03ba590dc751d4c5e0869fa4a7d2cecc161b8fc4d415cd680a6404a |
# Author: Samuel Genheden samuel.genheden@gmail.com
"""
This script uses the encore library
"""
import copy
import argparse
import numpy as np
import MDAnalysis as md
import encore
from encore.similarity import harmonic_ensemble_similarity, bootstrap_coordinates
class MyEnsemble(encore.Ensemble) :
def get_coordi... | SGenheden/Scripts | Projects/Orderparam/calc_heshalf.py | Python | mit | 2,936 | [
"MDAnalysis"
] | 2f13fc50f353e89bde622145ecdf6f97bbf22b29f4635c0b12887c9c5ccf45a6 |
# Copyright 2010-2017, The University of Melbourne
# Copyright 2010-2017, Brian May
#
# This file is part of Karaage.
#
# Karaage 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... | brianmay/karaage | karaage/people/urls/groups.py | Python | gpl-3.0 | 1,116 | [
"Brian"
] | ba65a069bbed9220673bdd2e634dcbe8a51a8fd51c80e833017e8050ed4c4275 |
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import os, subprocess
import dialog
from io import BytesIO
from zeroinstall import _
from zeroinstall.injector import model, selections, qdom
from gui import glib
XMLNS_0COMPILE = 'http://zero-install.sourceforge.n... | rammstein/0install | zeroinstall/0launch-gui/compile.py | Python | lgpl-2.1 | 3,234 | [
"VisIt"
] | f7513fe9f034d609c46216409e3d68c0ac5d8682c86745d23fc0dbdbf2842f38 |
# -*- coding: utf-8 -*-
from datetime import datetime, timedelta
from django.conf import settings
from django.core import mail
from django.core.files.storage import default_storage as storage
from django.utils import translation
import pytest
from mock import Mock, patch
from pyquery import PyQuery as pq
from olymp... | lavish205/olympia | src/olympia/reviewers/tests/test_utils.py | Python | bsd-3-clause | 54,345 | [
"VisIt"
] | 291ec563acb0ce2b835356b0d34ff5bbe591aa0199a51f099db3e8af320fb29a |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import logging
from peewee import fn
import time
from progressbar import ProgressBar, Percentage, Bar, ETA, Counter, RotatingMarker
from fetch.api import make_request, default_requests_session
from models import SlantTopic, Viewpoi... | andrewhead/Package-Qualifiers | fetch/slant_topics.py | Python | mit | 5,067 | [
"VisIt"
] | 38dd038268ea685635d6c795a2bdbaab9f00fd24b43a05c20cb6be8d5c9e9317 |
import alhazen.correlation_functions as corr
import numpy as np
ntheta = 100
flavor = 'cltt'
lmin = 100
lmax = 3000
ells = np.arange(lmin,lmax)
clCMB = np.ones(ells.size)
clpp = np.ones(ells.size)
clCMB_lensed = np.ones(ells.size)
accurate_lensing = True
compute_tgradt = True
l2range = list(range(lmin,lmax))
l2dim ... | msyriac/alhazen | tests/test_gradt.py | Python | gpl-3.0 | 8,244 | [
"Gaussian"
] | 6c483f16a699d9bb3e89a636077785cc0343443292904c3d8510e268eaef689f |
"""Collection of DIRAC useful list related modules.
By default on Error they return None.
"""
__RCSID__ = "$Id$"
import random
random.seed()
def uniqueElements(aList):
"""Utility to retrieve list of unique elements in a list (order is kept).
:param aList: list of elements
:type aList: python:list
:retur... | petricm/DIRAC | Core/Utilities/List.py | Python | gpl-3.0 | 3,397 | [
"DIRAC"
] | d6d08cef9d30a9a112409bf170fc9c22697a08960987cb842e10ac1f98658c2e |
#!/usr/bin/env python
## category Conversion
## desc Extract BED regions from a reference FASTA file
'''
Extract BED regions from a reference FASTA file.
Note: Sequences that are extracted will be in the same orientation as the
BED region, unless the {-ns} option is given.
'''
import sys
import os
from ngsutils.bed i... | ngsutils/ngsutils | ngsutils/bed/tofasta.py | Python | bsd-3-clause | 2,685 | [
"pysam"
] | 69f4619a4d280b2f661ef855dc27c1df6695059578efb3f2d0809707dcfa427f |
# -*- 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
from django.views import defaults as default_views
from pe... | jlmadurga/permabots-www | config/urls.py | Python | mit | 8,926 | [
"VisIt"
] | 344880983d19ca18dab43e0a9f4ac2107b4b41fa08c90686e77c45db7b6aca81 |
try: paraview.simple
except: from paraview.simple import *
from paraview.simple import *
paraview.simple._DisableFirstRenderCameraReset()
soln_pvd = GetActiveSource()
Calculator2 = Calculator()
RenderView1 = GetRenderView()
DataRepresentation1 = GetDisplayProperties(soln_pvd)
DataRepresentation4 = Show()
DataRepres... | davidshepherd7/oomph-lib-micromagnetics | etc/paraview_helpers/hms_vec.py | Python | gpl-2.0 | 1,786 | [
"ParaView"
] | aceb4ed418eae2687d92fe4656f3f719715c9789579f096a4f72b103441e4b78 |
from distutils.core import setup
from setuptools import find_packages
from sistr.version import __version__
classifiers = """
Development Status :: 4 - Beta
Environment :: Console
License :: OSI Approved :: Apache Software License
Intended Audience :: Science/Research
Topic :: Scientific/Engineering
Topic :: Scientifi... | peterk87/sistr_cmd | setup.py | Python | apache-2.0 | 1,646 | [
"BLAST"
] | af2b39557a415b766709e6e4f309df4ba18ccc5d160eb428212fcb1b41a32de4 |
pythons = {
'Chapman' : 'Graham',
'Cleese' : 'John',
'Idle' : 'Eric',
'Jones': 'Terry',
'Palin': 'Michael',
}
pythons['Gilliam'] = 'Gerry'
pythons['Gilliam'] = 'Terry'
others = {'Marx' : 'Groucho', 'Howard' : 'Moe'}
pythons.update(others)
del pythons['Marx']
del pythons['Howard']
a = python... | serggrom/python-projects | Part3.py | Python | gpl-3.0 | 3,902 | [
"MOE"
] | e4db0db9dac61d35ce1b1a0982a3169e440fcd35fe0493049ec8306de7e4d7c4 |
"""
This is a sample implementation for working DGL with DeepChem!
"""
import torch
import torch.nn as nn
import torch.nn.functional as F
from deepchem.models.losses import Loss, L2Loss, SparseSoftmaxCrossEntropy
from deepchem.models.torch_models.torch_model import TorchModel
class CGCNNLayer(nn.Module):
"""The co... | deepchem/deepchem | deepchem/models/torch_models/cgcnn.py | Python | mit | 13,277 | [
"CRYSTAL",
"pymatgen"
] | 3974b263acc82729d4f1ef7cca3e6e30ffba140aa0e4d6f440f3397908a2c71c |
#
# Copyright (c) 2017 Intel Corporation
# SPDX-License-Identifier: BSD-2-Clause
#
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 numba
from numba import njit, stencil
from numba.core.utils import ... | cpcloud/numba | numba/tests/test_stencils.py | Python | bsd-2-clause | 98,211 | [
"VisIt"
] | ffed9ebab5c60a24cd8ebc5f62cd988c4c67a6b177a2d5870ea1baf4605b9c4d |
##################################################################
# Copyright 2018 Open Source Geospatial Foundation and others #
# licensed under MIT, Please consult LICENSE.txt for details #
##################################################################
import lxml.etree
from werkzeug.test import Client
... | tomkralidis/pywps | pywps/tests.py | Python | mit | 5,694 | [
"NetCDF"
] | a4b69406140c0e9e03bfa4e63c8362edd6835398a6eca4d4722d6fecab8da88e |
# This is a modification of GPflow/vgp.py by Keisuke Fujii.
#
# The original source file is distributed at
# https://github.com/GPflow/GPflow/blob/master/GPflow/svgp.py
#
# 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... | fujii-team/GPinv | GPinv/stvgp.py | Python | apache-2.0 | 8,670 | [
"Gaussian"
] | 8f8cee003baa6daa30f20d5db9c1e293004a3d7fe99909d4cd4bb36363242f68 |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# This script shows the result of an ideal highpass filter in spatial domain
# Image pipeline
createReader = vtk.vtkImageReader2Factory()
reader = createReader.CreateImageRe... | hlzz/dotfiles | graphics/VTK-7.0.0/Imaging/Core/Testing/Python/IdealHighPass.py | Python | bsd-3-clause | 1,105 | [
"VTK"
] | 55fd4b5d8dc498ed19afc2d4af8cd786040dca1c8e1432cc2f41f8851717ea64 |
###
### GPAW benchmark: Carbon Nanotube
###
from __future__ import print_function
from gpaw.mpi import size, rank
from gpaw import GPAW, Mixer, PoissonSolver, ConvergenceError
from gpaw.occupations import FermiDirac
try:
from ase.build import nanotube
except ImportError:
from ase.structure import nanotube
try:... | mlouhivu/gpaw-accelerator-benchmarks | carbon-nanotube/input.py | Python | mit | 1,861 | [
"ASE",
"GPAW"
] | 321276664b823418772c37b910bbca7ac6c1731b7dfea717fe88b153d152c233 |
#!/usr/bin/env python
# import modules
from netCDF4 import Dataset as nc
from optparse import OptionParser
import os, stat, datetime, csv, re
from collections import OrderedDict as od
from numpy import zeros, array, concatenate, savetxt, double, logical_and
# search for patterns in variable list
def isin(var, varlist... | glotter/psims | data/tapps/psims2dly.py | Python | agpl-3.0 | 5,653 | [
"NetCDF"
] | 26b4c9117dd4bbc3f7994bd8b8c6cd618de0248ccbcd4ad7dc063f432aa96865 |
# --------------------------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See License.txt in the project root for license information.
# --------------------------------------------------------------------... | yugangw-msft/azure-cli | src/azure-cli/azure/cli/command_modules/storage/_validators.py | Python | mit | 87,495 | [
"VisIt"
] | 2bb88edaf11b5323a89caaaaef57088dc8e7bd8fecaf519e1d417d0ceb8773b7 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
AUTHOR
Pedro Cerqueira
github: @pedrorvc
DESCRIPTION
This script serves to create xml files contaning the information necessary
for the execution of BRIG (Blast Ring Image Generator), reducing the time
performing the tedious task of setting u... | TAMU-CPT/galaxy-tools | tools/genome_viz/brigaid.py | Python | gpl-3.0 | 36,126 | [
"BLAST",
"Biopython"
] | 5425645f852becaeb43c78c4feafd26722e00b0ba5a63d49540e1aa08ca01096 |
# -*- coding: utf-8 -*-
#
# escpos/impl/epson.py
#
# Copyright 2015 Base4 Sistemas Ltda ME
#
# 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
#... | base4sistemas/pyescpos | escpos/impl/epson.py | Python | apache-2.0 | 23,294 | [
"VisIt"
] | b7af3798723994a309b0d0ceeb6c519d4c8ed161aa20adfd7f7ca9c08d95eb01 |
'''
IMPORTANT NOTES:
In the .oms file, the first and last RA/DEC represent a reference slit at the bottom of the mask and the center of the mask respectively.
Please list the calibration lamp(s) used during your observations here
'''
cal_lamp = ['Xenon','Argon'] #'Xenon','Argon','HgNe','Neon'
print 'Using calibration ... | giffordw/OSMOSreduce | OSMOSreduce.py | Python | bsd-3-clause | 40,034 | [
"Galaxy"
] | f46b41c4b7008ee159f6af5524e90536a361a3d03f34dbda4856b92ad1e80c3e |
# Copyright 2013-2017, Brian May
#
# This file is part of python-alogger.
#
# python-alogger 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 ver... | Karaage-Cluster/python-alogger | alogger/parsers/slurm.py | Python | gpl-3.0 | 12,468 | [
"Brian"
] | 2fa0ac787e17353dacc6e6c5155aab9f607ddb8c9338c41c0ee63bc2e4854b40 |
# -*- coding: utf-8 -*-
"""
Created on Fri Aug 19 21:29:43 2016
@author: manon
"""
import numpy as np
import csv
from lien_apriori import dataFromFile,runApriori,printResults
from echantillonnage_apriori import echantillonnage,echantillonnage_glucose
from Bayesian_method import Bayesian_method
data_labels=['Homocy... | manonverdier/Bayesian_Network | simulated_annealing_test.py | Python | gpl-3.0 | 5,309 | [
"Cytoscape"
] | 89e938a927cfd6989663a01dd1d12619a8f13a99d9013eb5461a4f8f67a6ac9b |
#!/usr/bin/env python
'''
'''
__docformat__ = 'restructuredtext'
__version__ = '$Id: $'
import platform
from pyglet.gl.base import Config, CanvasConfig, Context
from pyglet.gl import ContextException
from pyglet.gl import gl
from pyglet.gl import agl
from pyglet.canvas.cocoa import CocoaCanvas
from pyglet.libs.d... | adamlwgriffiths/Pyglet | pyglet/gl/cocoa.py | Python | bsd-3-clause | 9,549 | [
"Jaguar"
] | 134060f1e8ac3618f92e708200d291fcad579d450b987d7347b0ca707dff2e82 |
from __future__ import print_function
from copy import deepcopy as dc
import numpy as np
from ase.io.trajectory import Trajectory
from ase.optimize.optimize import Optimizer
from numpy.random import RandomState
from pyiid.adp import has_adp
__author__ = 'christopher'
def leapfrog(atoms, step, center=True):
""... | CJ-Wright/pyIID | pyiid/sim/__init__.py | Python | bsd-3-clause | 3,830 | [
"ASE"
] | fc561c20ce39fd2aa6f05ffbc611580913d131a46a532af3a8daf28af567fde0 |
# Copyright 2013 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
import os
import logging
import unittest
from telemetry.core import util
from telemetry.core.platform.profiler import perf_profiler
from telemetry.unittest i... | mogoweb/chromium-crosswalk | tools/telemetry/telemetry/core/platform/profiler/perf_profiler_unittest.py | Python | bsd-3-clause | 2,072 | [
"VisIt"
] | 0be4cab768dc931c56f06e7708d85c3221e4783e96a7234b74d61f17441ee56f |
from logging import getLogger
try:
import xml.etree.cElementTree as et
except:
import xml.etree.ElementTree as et
try:
from galaxy.model import Job
job_states = Job.states
except ImportError:
# Not in Galaxy, map Galaxy job states to Pulsar ones.
from galaxy.util import enum
job_states = en... | ssorgatem/pulsar | pulsar/managers/util/cli/job/torque.py | Python | apache-2.0 | 3,802 | [
"Galaxy"
] | dc16f14308c3c82ff70e383f64539de4ec27244e3548ab319b422b3f12f5fcbe |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# Mip Agent
#
# @author Simon Andreas Frimann Lund
#
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the GNU Gene... | heromod/migrid | mig/vm-proxy/deprecated/proxy/mipagent.py | Python | gpl-2.0 | 1,429 | [
"Brian"
] | c9273c7d7ec7d6f3a58bc8144401ae060a34e132491ced77884f6ecc91f5def0 |
import cv2
import numpy as np
from matplotlib import pyplot as plt
class Thresholding:
def __init__(self):
return
def simple(self,img):
thresh = 50
ret,thresh1 = cv2.threshold(img,thresh,255,cv2.THRESH_BINARY)
ret,thresh2 = cv2.threshold(img,thresh,255,cv2.THRESH_BINARY... | LevinJ/CodeSamples | imageprocessing/thresholding/thresholding.py | Python | gpl-2.0 | 3,784 | [
"Gaussian"
] | c13b33ca199fa6561c3768fb7ad9525cea495774518a506139167bdc5fe442cb |
import array
from MB import music
from util import dlinkedlist
debug=True
class Phrase:
"""
Defines the head and tail within a list of events.
events in the list should have a
ev.time --- time of event
ev.data --- (toks,data)
"""
def __init__(self,head,tail):
s... | pauljohnleonard/MusicBox | src/MB/players.py | Python | gpl-2.0 | 16,489 | [
"VisIt"
] | abcad2776e1c65d2705218d2f4521c0643a9626c43f2533aa2e559995c8b6929 |
# Sample module in the public domain. Feel free to use this as a template
# for your modules (and you can remove this header and take complete credit
# and liability)
#
# Contact: Brian Carrier [carrier <at> sleuthkit [dot] org]
#
# This is free and unencumbered software released into the public domain.
#
# Anyone is f... | dgrove727/autopsy | pythonExamples/fileIngestModuleWithGui.py | Python | apache-2.0 | 8,201 | [
"Brian"
] | 0848768f465eabd1f4f68904cd8db5c3f47df3c819a9f8aed70a0aaf4b92da36 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# gridstat - [insert a few words of module description on this line]
# Copyright (C) 2003-2009 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of ... | heromod/migrid | mig/shared/gridstat.py | Python | gpl-2.0 | 22,530 | [
"Brian"
] | c4881563b4255d96954f2c590aa1d5dce250e6767a3485c47c80004c3278a70b |
# Copyright (C) 2015-2021 The Software Heritage developers
# See the AUTHORS file at the top-level directory of this distribution
# License: GNU General Public License version 3, or any later version
# See top-level LICENSE file for more information
import datetime
import logging
import random
import select
from typi... | SoftwareHeritage/swh-storage | swh/storage/postgresql/db.py | Python | gpl-3.0 | 48,474 | [
"VisIt"
] | 141143d439144daef6be240cf79482264612f6f365c28ab42cd768406d84c62d |
# 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 RBumphunter(RPackage):
"""Bump Hunter.
Tools for finding bumps in genomic data"""
... | rspavel/spack | var/spack/repos/builtin/packages/r-bumphunter/package.py | Python | lgpl-2.1 | 1,713 | [
"Bioconductor"
] | edf7a751b6ce53f70cb219189b31397788406289f1f12891a861eb8f1910a5c5 |
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://setuptools.readthedocs.io/en/latest/easy_install.html
"""
from glob import gl... | RalfBarkow/Zettelkasten | venv/lib/python3.9/site-packages/setuptools/command/easy_install.py | Python | gpl-3.0 | 86,430 | [
"VisIt"
] | 94c4cc05bc2c35d7fbbd83898cf0996025015d5a8eccab1df8d084d15efa7675 |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2003-2011 Edgewall Software
# Copyright (C) 2003-2007 Jonas Borgström <jonas@edgewall.com>
# All rights reserved.
#
# This software is licensed as described in the file COPYING, which
# you should have received as part of this distribution. The terms
# are also available at htt... | moreati/trac-gitsvn | trac/env.py | Python | bsd-3-clause | 38,387 | [
"VisIt"
] | b9f02baeece5235d7257d58e5b984cb5e979db004638f424fcaaa9dc32ece164 |
#!/usr/bin/env python
'''
setup board.h for chibios
'''
import argparse
import sys
import fnmatch
import os
import dma_resolver
import shlex
import pickle
import re
import shutil
parser = argparse.ArgumentParser("chibios_pins.py")
parser.add_argument(
'-D', '--outdir', type=str, default=None, help='Output directo... | squilter/ardupilot | libraries/AP_HAL_ChibiOS/hwdef/scripts/chibios_hwdef.py | Python | gpl-3.0 | 70,394 | [
"CRYSTAL"
] | 83feecc19cb93108eefc18d21d511bf11bcc358f496bf7286f03305ff8462bfb |
# -*- coding: utf-8 -*-
"""
sphinx.quickstart
~~~~~~~~~~~~~~~~~
Quickly setup documentation source to work with Sphinx.
:copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
from __future__ import print_function
from __future__ import absolute... | neerajvashistha/pa-dude | lib/python2.7/site-packages/sphinx/quickstart.py | Python | mit | 52,767 | [
"VisIt"
] | 60935a1158ab15f1422bbf7cf86db0aa4b2d10099c8dd821c547ef2a47dc5c34 |
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