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#!/usr/bin/env python
#=============================================================================================
# MODULE DOCSTRING
#=============================================================================================
"""
Test YAML functions.
"""
#=======================================================... | jchodera/yank | Yank/tests/test_yaml.py | Python | lgpl-3.0 | 78,332 | [
"Gromacs",
"MDTraj",
"OpenMM"
] | 8b562283ffaa298bd7773da7d4e8f25fac441aad71f9b171e0e21eea505cc2ad |
#
# Copyright (C) 2013,2014,2015,2016 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... | lahnerml/espresso | testsuite/python/cellsystem.py | Python | gpl-3.0 | 1,626 | [
"ESPResSo"
] | 95200e90a5e254f7fd4328a595ff0256062cdd7bb0b423976092eea78a24e8e5 |
# 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 atexit
import logging
import re
from devil.android import device_errors
logger = logging.getLogger(__name__)
_atexit_messages = set()
# Defines how... | catapult-project/catapult | devil/devil/android/perf/perf_control.py | Python | bsd-3-clause | 16,185 | [
"Galaxy"
] | eca164a6758916f7b988df698d45499160a53a46244782f83e86068e898efd3e |
# 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 atexit
import logging
from pylib import android_commands
from pylib.device import device_utils
class PerfControl(object):
"""Provides methods for ... | collinjackson/mojo | build/android/pylib/perf/perf_control.py | Python | bsd-3-clause | 6,284 | [
"Galaxy"
] | 36a0c97befb1c66adcbff399e657f55aae6bfbb786d58d2e32e39129bd95ff8f |
import numpy as np
import cv2
import sys
def uso():
print 'Erro: nao foi possivel abrir a imagem fornecida'
print 'Uso: python2 ' + sys.argv[0] + ' src dst'
sys.exit()
def salt_and_pepper(src, a, b, Pa=0, Pb=255):
dst = np.copy(src)
for i in range(dst.shape[0]):
for j in range(dst.shape[1]... | rerthal/mc920 | proj07/proj07.py | Python | gpl-3.0 | 1,884 | [
"Gaussian"
] | 89047028771a3e879f4aea85fcb8e219983c3dafe06e590176d0d2404db3f2bc |
"""
Compatibility package with the high-level API of PyEVTK.
This package is meant as a drop-in replacement for high-level functions of
PyEVTK. However, it does not reproduce exactly the behavior of PyEVTK, most
notably:
- uvw.Writer keyword arguments (such as compression=True) can be passed to
the functions
- Data... | prs513rosewood/uvw | uvw/dropin/hl.py | Python | mit | 14,613 | [
"VTK"
] | 98d922fb6c80f110e58c06cb4880876245e0c30e0bb6e83144f2966bd7cc009c |
# pre_NAMD.py
# Creates the files used for NAMD based on the .pdb file dowloaded from PDB bank
#
# Usage:
# python pre_NAMD.py $PDBID
#
# $PDBID=the 4 characters identification code of the .pdb file
#
# Input:
# $PDBID.pdb: .pdb file downloaded from PDB bank
#
# Output:
# $PDBID_p.pdb: .pdb file with water mole... | Xiaofei-Zhang/NAMD_Docking_pipeline | pre_NAMD/pdb_to_psf.py | Python | mit | 1,736 | [
"NAMD",
"VMD"
] | c977c9765f1dbd46182ea3da0f85312d7f02529433c080b10472d2ac4229cabb |
# 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... | KaiSzuttor/espresso | testsuite/python/rotational_inertia.py | Python | gpl-3.0 | 6,230 | [
"ESPResSo"
] | 0aa41c27f6a325752b37e7b512f18e0002ab57bfcf39a3727c6a7a6ab3200d1f |
"""Import tasks for GAIA."""
import csv
import os
import re
from astrocats.catalog.utils import jd_to_mjd, pbar
from decimal import Decimal
from ..supernova import SUPERNOVA
def do_gaia(catalog):
"""Import from the GAIA alerts page."""
task_str = catalog.get_current_task_str()
fname = os.path.join(cata... | astrocatalogs/supernovae | tasks/gaia.py | Python | mit | 4,220 | [
"Galaxy"
] | 2e5355c12ee576bba2717f48ddcd071e9d2dd654291a58d0757f9254bd3d0b4c |
# -*- coding: utf-8 -*-
"""
Generate centreline and write it out as .vtk legacy format.
"""
import os
import sys
# Run in current directory.
os.chdir(os.path.dirname(os.path.abspath(__file__)))
# Import path for the CentrelineGenerator script.
importPath = os.path.abspath(os.path.join(os.path.dirname(__file__), '../... | BlueFern/DBiharMesher | meshes/c512/Generate512Centreline.py | Python | gpl-2.0 | 975 | [
"VTK"
] | 52781b8815741cc74ecd13a78964de20d1a7e0b2737160d42c8cd4362baa36fe |
""" Variable Unittest. """
import cwt, os
# datainputs = """[domain=[{"name":"d0","lat":{"start":70,"end":90,"system":"values"},"lon":{"start":5,"end":45,"system":"values"}}],
# variable=[{"uri":"file:///dass/nobackup/tpmaxwel/.edas/cache/collections/NCML/MERRA_TAS1hr.ncml","name":"tas:v1","domain":"d0"}],
# operatio... | nasa-nccs-cds/EDAS | python/test/localPerformanceTests/DASS_CWTPythonClientTest.py | Python | gpl-2.0 | 1,508 | [
"Gaussian"
] | f1c72a0928eb9e6f7ed0cd2c69b0967f2f44f753360efc1f123629b5733c3044 |
"""
A number of argparse helpers, generally using custom argument typing for
additional input value transformations.
"""
import argparse
import re
import sys
from typing import List, Tuple, Union
def add_standard_params(parser: argparse.ArgumentParser) -> None:
"""
Adds -v, -p and -t.
"""
parser.add_a... | sibis-platform/sibis | cli.py | Python | bsd-3-clause | 5,215 | [
"VisIt"
] | 9ebdb37aa2a78480b289f381b90012d1f345e748136bdf884185ba1cdb1b3c47 |
# -*- coding: utf-8 -*-
# This file is part of Shuup.
#
# Copyright (c) 2012-2021, Shuup Commerce Inc. All rights reserved.
#
# This source code is licensed under the OSL-3.0 license found in the
# LICENSE file in the root directory of this source tree.
import os
import pytest
import time
from django.test.utils import ... | shoopio/shoop | shuup_tests/browser/front/test_xtheme_plugin_form.py | Python | agpl-3.0 | 9,875 | [
"VisIt"
] | 2a936da4407b944ce36724b68f59ce1bc84103c4f30dc969b698ff1f59d2b725 |
import sys
sys.path.insert(1, "../../")
import h2o
def get_model_test(ip,port):
# Connect to h2o
h2o.init(ip,port)
prostate = h2o.import_frame(path=h2o.locate("smalldata/logreg/prostate.csv"))
r = prostate[0].runif()
train = prostate[r < 0.70]
test = prostate[r >= 0.70]
# Regression
... | ChristosChristofidis/h2o-3 | h2o-py/tests/testdir_misc/pyunit_get_model.py | Python | apache-2.0 | 2,421 | [
"Gaussian"
] | 8e188de430d0e61163cbda5a0933fc0264fb78d3d6de45fc2e10d910f165c132 |
"""This demo solves the Stokes equations, using quadratic elements for
the velocity and first degree elements for the pressure (Taylor-Hood
elements). The sub domains for the different boundary conditions
used in this simulation are computed by the demo program in
src/demo/mesh/subdomains."""
# Copyright (C) 2007 Kris... | alogg/dolfin | demo/undocumented/stokes-taylor-hood/python/demo_stokes-taylor-hood.py | Python | gpl-3.0 | 2,540 | [
"VTK"
] | 5c378175855faa55c264b50a5ab2273350b64b42b237b5869052d564c9db14b4 |
# Script Version: 1.0
# Author: Tsz Kwong Lee
# Project: AMA3D
# Task Step: 4
# This script use information from PDB to select the best CATH topology representative among all homologous domains.
# CathDomainList File format: CLF format 2.0, to find more info, please visit www.cathdb.info
# R observed - Residual facto... | teheavy/AMA3D | Nh3D/4_CathBestTopo_filter_V2.1.py | Python | gpl-2.0 | 16,076 | [
"VisIt"
] | 8fa373633c428a5d14b0ec067e0f4617a60334bc3698a37af2e16907fc7e5f43 |
# Copyright 2012 by Wibowo Arindrarto. 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.
"""Bio.SearchIO parser for HMMER table output format."""
from itertools import chain
fro... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/SearchIO/HmmerIO/hmmer3_tab.py | Python | apache-2.0 | 12,539 | [
"Biopython"
] | 27eec85b9740a91ad866e392288c0da51c7fa41ab3b4bd5303e9c2bfb79d3021 |
#! /usr/bin/python
#
# Copyright (C) 2003-2014 ABINIT group
#
# Written by Matthieu Verstraete in python (compatible v1.9).
# This is free software, and you are welcome to redistribute it
# under certain conditions (GNU General Public License,
# see ~abinit/COPYING or http://www.gnu.org/copyleft... | SamKChang/abinit-7.10.5_multipole | scripts/pre_processing/tokenize_file.py | Python | gpl-3.0 | 2,175 | [
"ABINIT"
] | f3fa19858cc3035ace25fede2acd6dfeeac5bc4265721b75ed3b5018ad8827d5 |
import operator
from functools import reduce
def get(caves, i, j):
if i < 0 or i >= len(caves):
return None
if j < 0 or j >= len(caves[i]):
return None
return caves[i][j]
modifiers = [
(-1, 0),
(1, 0),
(0, -1),
(0, +1)
]
with open("inputs/day9.txt") as f:
caves = []
... | astonshane/AdventOfCode | 2021/day9.py | Python | mit | 1,915 | [
"VisIt"
] | 03740afade353fa6f4ddea5308be17ef6d792986d5aaaaea11c1e9934365898f |
"""
This module contains classes related to data visualization and rendering.
**Rendering:**
* :py:class:`RenderSettings`
* :py:class:`Viewport`
* :py:class:`ViewportConfiguration`
**Render engines:**
* :py:class:`OpenGLRenderer`
* :py:class:`TachyonRenderer`
* :py:class:`POVRayRenderer`
**Data visuali... | srinath-chakravarthy/ovito | src/plugins/pyscript/python/ovito/vis/__init__.py | Python | gpl-3.0 | 5,082 | [
"OVITO"
] | 64626d00d3a34ed7a1d8d8a2c9bde3f9c02727e2a6252b8f0b7d6ad652f77946 |
"""
This module reads and writes a series of data cubes to a NetCDF file.
=== Set up some parameters ===
Define the shape of the data cube.
>>> shape = (4, 5, 3)
>>> res = (1., 100., 200.)
Set the values of the data cube.
>>> var = numpy.random.random (shape)
Write cubes at these times.
>>> times = range (5)
This... | mdpiper/topoflow | topoflow/utils/nccs_files_Nio.py | Python | mit | 13,884 | [
"NetCDF"
] | 61ee564e6902c29950b9895da834790d6c88dd13d72b7f9bf39ee413a6efc4a1 |
#
# Copyright 2001 - 2016 Ludek Smid [http://www.ospace.net/]
#
# This file is part of Outer Space.
#
# Outer Space is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (... | ospaceteam/outerspace | client/osci/messages.py | Python | gpl-2.0 | 15,355 | [
"Galaxy"
] | 57dce0236d2b0c804c2d8f10580ed92e43b19e8fc0e20d910778ac09a77de905 |
# -*- coding: utf-8 -*-
##############################################################################
#
# OpenERP, Open Source Management Solution
# Copyright (C) 2004-2009 Tiny SPRL (<http://tiny.be>).
# Copyright (C) 2010-2014 OpenERP s.a. (<http://openerp.com>).
#
# This program is free software: you ca... | minhtuancn/odoo | openerp/tools/misc.py | Python | agpl-3.0 | 45,945 | [
"VisIt"
] | 0557a3e4ce8aa7cba44c2807f1deb5b23b4169f634ddd055528b2c5681abcf3e |
import cv2
import numpy
from PIL import Image
threshold = lambda *a: cv2.threshold(*a)[1]
def lut(frame, gamma_in=100, offset=0):
# gamma_in comes in as [0, 99], maps to [-2, 2]
# this lets the clipping happen more spectacularly
gamma = (gamma_in - 50) / 25.
lut = numpy.arange(256) * gamma
lut +... | natedileas/ImageRIT | Server/effects/config.py | Python | gpl-3.0 | 6,477 | [
"Gaussian"
] | 5a69f9f867a8a68b6e7da9660008c19f3d552b982961c2ea7cd4272d1daa7781 |
"""Boundary conditions for receptor based boundary conditions
including unbinding and rebinding.
"""
from collections import defaultdict
import logging
import itertools as it
import time
import numpy as np
from geomm.grouping import group_pair
from geomm.superimpose import superimpose
from geomm.rmsd import calc_rm... | ADicksonLab/wepy | src/wepy/boundary_conditions/receptor.py | Python | mit | 25,643 | [
"MDTraj"
] | fd419c589ef01a3ecb8042be60af22cbac55bafaa7f422db06c088fa9b2a1bd1 |
# -*- encoding: utf-8 -*-
'''
Created on Nov 12, 2014
@author: antonio
'''
import os, shlex, subprocess
class LatexReport(object):
'''
Clase representa un informe
'''
def __init__(self, title, author):
try:
os.mkdir("plots/") #Creo, si no esta, la carpeta en la que guardar las fig... | aydevosotros/TFG-AntonioMolina | TFG/benchmarks/ReportGenerator.py | Python | gpl-2.0 | 2,740 | [
"ASE"
] | 5dad94383e76134f89bf6b330c56262f7562755ff2213810498a6eada211e8a1 |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2020, 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.
"""Run data tests for cclib."""
import importlib
import logging
import os
import sys
import unittest
import cclib
__fi... | cclib/cclib | test/test_data.py | Python | bsd-3-clause | 12,415 | [
"ADF",
"Dalton",
"GAMESS",
"Gaussian",
"Jaguar",
"MOLCAS",
"MOPAC",
"Molpro",
"NWChem",
"ORCA",
"Psi4",
"TURBOMOLE",
"cclib"
] | d8bf2e55d30df48882957bfd3ff31baee0e16ae4e50d21ddc107a8cbccf03254 |
#
# Copyright (c) 2016 nexB Inc. and others. All rights reserved.
# http://nexb.com and https://github.com/nexB/scancode-toolkit/
# The ScanCode software is licensed under the Apache License version 2.0.
# Data generated with ScanCode require an acknowledgment.
# ScanCode is a trademark of nexB Inc.
#
# You may not use... | yasharmaster/scancode-toolkit | tests/licensedcode/license_test_utils.py | Python | apache-2.0 | 6,019 | [
"VisIt"
] | 6450e43d9e58feb8a0c773e62f1a7bc806ceaca2870ea077962b783be4086ce1 |
#
# Copyright 2016 The BigDL Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | intel-analytics/BigDL | python/orca/test/bigdl/orca/learn/ray/tf/test_ray_tf2estimator.py | Python | apache-2.0 | 3,429 | [
"ORCA"
] | f9cb0b8b08354ff714fbbb563d9e44206d2ae4c40bc904b7b377686be9bb67cb |
##############################################################################
# Medical Image Registration ToolKit (MIRTK)
#
# Copyright 2017 Imperial College London
# Copyright 2017 Andreas Schuh
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with ... | BioMedIA/MIRTK | Applications/lib/python/mirtk/atlas/spatiotemporal.py | Python | apache-2.0 | 77,515 | [
"Gaussian"
] | bbba6d101d164105ae27893a615fceee42acbb90e63ffe2d3f8f8776c3e140d2 |
# -*- coding: utf-8 -*-
# Copyright 2007-2021 The HyperSpy developers
#
# This file is part of HyperSpy.
#
# HyperSpy 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... | thomasaarholt/hyperspy | hyperspy/_components/voigt.py | Python | gpl-3.0 | 7,040 | [
"Gaussian"
] | 4de6edfca19108debfa5856787306a37d89e8d3683690c821567db56610abcba |
#!/usr/bin/env python3
# @package fill_missing
# @brief This script solves the Laplace equation as a method of filling holes in map-plane data.
#
# Uses an approximation to Laplace's equation
# @f[ \nabla^2 u = 0 @f]
# to smoothly replace missing values in two-dimensional NetCDF
# variables with the average of the ``... | pism/pism | util/fill_missing_petsc.py | Python | gpl-3.0 | 12,044 | [
"NetCDF"
] | f02b7fbe701d594d8baec5e1135b614d1aa8494b5f1cd702f8ab90ff349dd84a |
# Copyright (c) 2016, Mike Smith
# Licensed under the BSD 3-clause license (see LICENSE.txt)
import GPy
import numpy as np
import sys #so I can print dots
import time
import os
from joblib import Parallel, delayed
def get_log_likelihood(inputs,data,clust):
"""Get the LL of a combined set of clusters, ignoring time... | mikecroucher/GPy | GPy/util/cluster_with_offset.py | Python | bsd-3-clause | 9,193 | [
"Gaussian"
] | 503684b291517dc819ebd820ca3fc2d2438df439a938400374e5f22cfbf0725d |
# Orca
#
# Copyright (C) 2010-2011 The Orca Team
# Copyright (C) 2011-2012 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# 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; e... | ruibarreira/linuxtrail | usr/lib/python3/dist-packages/orca/scripts/toolkits/WebKitGtk/script.py | Python | gpl-3.0 | 25,412 | [
"ORCA"
] | fcfa6de85956b483601035cbf2de7d8e8fcf469b3b7ef2a0ede21577297db987 |
langversion = 1
langname = "English"
##updater
# text construct: "Versión "+version+available+changelog
#example: Version 3 available, click here to download, or for changelog click here
available = " disponible, haga clic aquí para descargar"
changelog = ", o para el registro de cambios haga clic aquí"
##world gen
w... | flying-sheep/omnitool | Language/spanish.py | Python | mit | 3,418 | [
"VisIt"
] | 6d5ae649b15c1e3d30a54d77d6c67e24e9e371b1edef30bfdb51650c73fabd23 |
#
# Copyright (C) 2001 greg Landrum
#
""" unit testing code for compound descriptors
"""
import unittest
from rdkit.ML.Descriptors import Parser
import math
class TestCase(unittest.TestCase):
def setUp(self):
self.piece1 = [['d1', 'd2', 's1'], ['d1', 'd2', 's1']]
self.aDict = {'Fe': {'d1': 1, 'd2': 2... | bp-kelley/rdkit | rdkit/ML/Descriptors/UnitTestParser.py | Python | bsd-3-clause | 1,864 | [
"RDKit"
] | 678735204371646ca055813e45e975a8d5607baea36e74725aa656e6b5fbe8fd |
# -*- coding: utf-8 -*-
#
# Pulsar documentation build configuration file, created by
# sphinx-quickstart on Sun Dec 16 23:16:23 2012.
#
# 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.
#
# All ... | ssorgatem/pulsar | docs/conf.py | Python | apache-2.0 | 7,849 | [
"Galaxy"
] | ceb4793d564bcd2491cc3cbd24031106513fbf501622e1686e42f10d48051d00 |
# This file is part of the myhdl library, a Python package for using
# Python as a Hardware Description Language.
#
# Copyright (C) 2003-2015 Jan Decaluwe
#
# The myhdl 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 t... | juhasch/myhdl | myhdl/conversion/_toVHDL.py | Python | lgpl-2.1 | 78,411 | [
"VisIt"
] | bbdc18264db5304f6fe0257f4ef3e1a30e4106e93a8db77c977429aea65cd046 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import unittest
import os
import json
import numpy as np
import warnings
import xml.etree.cElementTree as ET
from pymatgen.core.periodic_table import Element... | czhengsci/pymatgen | pymatgen/io/vasp/tests/test_outputs.py | Python | mit | 55,313 | [
"VASP",
"pymatgen"
] | aa2aa7a14e4e3f26fa067282a07391dd4484c4df5cba3df418d5565f9425d3f1 |
from pylab import *
import numpy as np
import pandas as pd
# from matplotlib.pyplot import plot,show,draw
import scipy.io
from functions import *
import _pickle as cPickle
import time
import os, sys
import ipyparallel
import neuroseries as nts
from numba import jit
data_directory = '/mnt/DataGuillaume/MergedData/'
da... | gviejo/ThalamusPhysio | python/main_make_decoding_swr.py | Python | gpl-3.0 | 13,745 | [
"Gaussian",
"NEURON"
] | 2971229f637db31b3bd039b4563f5fa0eb815b2359570202f35135d52f9cdb78 |
''' Plot animation of the Boomerang. '''
import numpy as np
import os
import sys
sys.path.append('..')
import vtk
import boomerang as bm
from config_local import DATA_DIR
from quaternion_integrator.quaternion import Quaternion
from general_application_utils import read_trajectory_from_txt
N_SPHERES = len(bm.M)
TIME_... | stochasticHydroTools/RotationalDiffusion | boomerang/plot_boomerang_trajectory.py | Python | gpl-3.0 | 5,789 | [
"VTK"
] | bc10eefe2c7aa18546ad9fbd4fc9e303b42cf0cf08b63266716fcd8da1b54da8 |
#!/usr/bin/python
# Copyright 2010 Doug Zongker
#
# 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 ... | nhaehnle/aiant | test/trueskill.py | Python | apache-2.0 | 13,012 | [
"Gaussian"
] | 8dc84005802b3ba14ac915f42997411966e001ac9139875591c066af5b1efa65 |
"""
Test basic molecular features.
"""
import numpy as np
import unittest
from rdkit import Chem
from vs_utils.features.basic import MolecularWeight, SimpleDescriptors
class TestMolecularWeight(unittest.TestCase):
"""
Test MolecularWeight.
"""
def setUp(self):
"""
Set up tests.
"""
smiles = ... | rbharath/vs-utils | vs_utils/features/tests/test_basic.py | Python | gpl-3.0 | 1,034 | [
"RDKit"
] | 14eb179c993fc70d240b6c6fa3b53cf8b38c39d13428166bd41f5c8d07a00c44 |
# coding: utf-8
from __future__ import print_function, division, absolute_import
from cutadapt.colorspace import encode, decode
from cutadapt.scripts.cutadapt import main
from .utils import run, datapath
# If there are any unknown characters in the test sequence,
# round tripping will only work if all characters afte... | Chris7/cutadapt | tests/testcolorspace.py | Python | mit | 4,096 | [
"BWA"
] | 41f26e3523f76ef168c546fa33908291e085bf09e43ee68a17acd15421438a5d |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import logging
from retools.limiter import Limiter as ReToolsLimiter
from octopus.limiter.in_memory.per_domain import Limiter as InMemoryPerDomainLimiter
class Limiter(InMemoryPerDomainLimiter):
def __init__(self, *domains, **kw):
limiter_miss_timeout_ms = ... | heynemann/octopus | octopus/limiter/redis/per_domain.py | Python | mit | 2,072 | [
"Octopus"
] | 75021185aa1d5cc6ee283f18eaf1d7e1fe13dde2f7dc28b9ac786a6e86bc4888 |
'''
Created on 5 Sep 2013
@author: Brian
===============================================================================
INETCOMMS has classes for communications over the internet
Supported features are:
CLASS FTPLINK:
Uploading data and video files to an FTP server
... | dcollins31/RSPiVT_EchoServer | inetcomms.py | Python | gpl-2.0 | 25,027 | [
"Brian"
] | 062a6d7f6b360215bd6b06328aa0101a99c004a014cd6c1ec1ac0bec6295a9a2 |
# This function returns the TSV file connected to a given FASTQ file
def getTSV(wildcards):
localFastq =''
if wildcards.fastq[-3:] == '_R1' or wildcards.fastq[-3:] == '-R1' or wildcards.fastq[-3:] == '_R2' or wildcards.fastq[-3:] == '-R2':
localFastq = wildcards.fastq[0:-3]
else:
localFastq ... | cbg-ethz/NGS-pipe | snake/common/align/align_snake.py | Python | apache-2.0 | 20,320 | [
"BWA"
] | f5816867709b902d1df463d8491ba29f09961393e714a0924920c01e2a2b803d |
import csv
import heapq
import numpy as np
from ase.tasks.io import read_json
ann_fontsize = 'small'
label_fontsize = 12
def most_common_value(values, precision=None):
import heapq
# find the most common value
if precision is not None:
vs = [round(v, precision) for v in values]
else:
... | grhawk/ASE | tools/ase/test/tasks/analyse.py | Python | gpl-2.0 | 14,783 | [
"ASE"
] | 7071be4074ed9896d4cffd1a57ec6536c43ce44263ef6deaa13f5c41526b4df5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
FIRtro 2.0 Módulo de gestión de presets usado por server_process.
Uso informativo en línea de comando:
presets.py [list | preset*] (*: detalla los que coincidan)
"""
# v1.1:
# - Permite indicar "dirac_pulse" en vías full range (en ese caso no existe un... | rripio/FIRtro | bin/presets.py | Python | gpl-3.0 | 9,550 | [
"DIRAC"
] | d7791637cea38a66c74b054cdafbbc80f5fc110144fe8dd187abb1d7bbf25f49 |
#!/usr/bin/python
from scipy.stats import cauchy
import random
import math
import csv
import numpy as np
import netCDF4 as nc
import argparse
import lvDiagram
'''
parser = argparse.ArgumentParser()
parser.add_argument("numberRegions", type=int,
help="Number of HII Regions to Populate in Model")
a... | WillArmentrout/galSims | simulate/Simulate_Function.py | Python | gpl-2.0 | 17,243 | [
"Galaxy",
"Gaussian"
] | 64e33f04e5c41130d2175f553ef1662a9a7b90e16148e44a0b43405268797689 |
"""semi-views for the `group_messaging` application
These are not really views - rather context generator
functions, to be used separately, when needed.
For example, some other application can call these
in order to render messages within the page.
Notice that :mod:`urls` module decorates all these functions
and turn... | maxwward/SCOPEBak | group_messaging/views.py | Python | gpl-3.0 | 8,583 | [
"VisIt"
] | ba8e6ec063370cd7294658993b908d99edbb5663642155d361bca4c80b3a56bb |
##############################################################################
# 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/vtkh/package.py | Python | lgpl-2.1 | 4,051 | [
"VTK"
] | a94952e9456274901154448af3b98074cde170a69c0197f5335b1c7ca0649fb8 |
#!/usr/bin/env python
##~---------------------------------------------------------------------------##
## _______ _______ _______ _ _ ##
## | _ || || || | _ | | ##
## | |_| || || _ || || |... | AmazingCow/COWTODO | cowtodo.py | Python | gpl-3.0 | 26,961 | [
"VisIt"
] | dbcffa75366987053337fe0d4425778cff6ff83b14fba7e2ef58c7a4fc6d9432 |
#
# Angel Farguell, CU Denver
#
from __future__ import absolute_import
import logging
import re
import glob
import json
import subprocess
import os.path as osp
from datetime import datetime, timedelta
import pytz
import numpy as np
import netCDF4 as nc
from utils import Dict, split_path, utc_to_utcf, ensure_dir
from i... | openwfm/wrfxpy | src/ingest/sat_source_aws.py | Python | mit | 12,986 | [
"NetCDF"
] | 2fe7b1f4c93fca58ed53e16d96da7d0df988718c1b19fdee8c2a7b3b49471752 |
import datetime
import glob
import os
import random
import subprocess
import uuid
import pyproj
import xarray
from clover.geometry.bbox import BBox
from clover.netcdf.describe import describe
from clover.render.renderers.stretched import StretchedRenderer
from clover.render.renderers.unique import UniqueValuesRenderer... | consbio/landscapesim | landscapesim/common/services.py | Python | bsd-3-clause | 18,215 | [
"NetCDF"
] | 6f2141b4c4f21e29b8002eefe75d258e08639d2a8babfc8ff6ec33083561ec4a |
#!/usr/bin/python
import subprocess as sp, argparse
parser=argparse.ArgumentParser()
parser.add_argument('--mei',nargs='*')
parser.add_argument('--option_tag',nargs='*')
parser.add_argument('--path',nargs='*')
args=parser.parse_args()
insertME=''.join(args.mei)
option_tag=''.join(args.option_tag)
path_current=''.joi... | JXing-Lab/ME-SCAN-SVA | modules/JW_producing_all_insertion_with_ind_info.py | Python | gpl-3.0 | 3,773 | [
"BLAST"
] | adba3667e752802ffbf8ad462b74077abd7fccb8fd29803e18c7773595c791f8 |
#!/usr/bin/env python
###########################
###### IMPORT MODULES
###########################
import LCSbase as lb
import LCScommon as lcscommon
from matplotlib import pyplot as plt
from mpl_toolkits.axes_grid1 import make_axes_locatable
import matplotlib.gridspec as gridspec
import numpy as np
import os
impo... | rfinn/LCS | python/lcs_paper2.py | Python | gpl-3.0 | 156,757 | [
"Galaxy"
] | 54a1323c9d2b7fe29b7cc02a2dbd91903fa8779f59351e556f7ab4bddaf8deec |
# https://leetcode.com/problems/binary-tree-longest-consecutive-sequence/
# Definition for a binary tree node.
# class TreeNode(object):
# def __init__(self, x):
# self.val = x
# self.left = None
# self.right = None
# This algorithm is basically a graph DFS algorithm that traverses the tre... | young-geng/leet_code | problems/298_binary-tree-longest-consecutive-sequence/main.py | Python | mit | 1,474 | [
"VisIt"
] | bffa6bc28040f4d184b8658482f0fdfcab1ed80919f2aac8dfed4a719a3ad4cb |
#----------------------------------
#Lab8.py
#Brian O'Dell
#October 24, 2016
#All that is needed to run this file is to type
#python Lab8.py
#the file needs to be in the current path in the terminal
#
#This program will take a truth table that the user enters
#and construct the appropriate conjunctive normal form,
#and... | brian-o/CS-CourseWork | CS278/Lab8/Lab8.py | Python | gpl-3.0 | 2,407 | [
"Brian"
] | 607f043d28895cf94708b3221c2168babc26f833fef704ac3feaba370ee7507e |
# -*- coding: utf-8 -*-
"""
pysteps.noise.utils
===================
Miscellaneous utility functions related to generation of stochastic perturbations.
.. autosummary::
:toctree: ../generated/
compute_noise_stddev_adjs
"""
import numpy as np
try:
import dask
dask_imported = True
except ImportError:... | pySTEPS/pysteps | pysteps/noise/utils.py | Python | bsd-3-clause | 4,181 | [
"Gaussian"
] | 57f5d9f9c2a856a374ea0c2e96b2074970696bdf09a6e1a839f323eb3f88a475 |
# Copyright (c) 2015 the GPy Austhors (see AUTHORS.txt)
# Licensed under the BSD 3-clause license (see LICENSE.txt)
from .bayesian_gplvm import BayesianGPLVM
class DPBayesianGPLVM(BayesianGPLVM):
"""
Bayesian Gaussian Process Latent Variable Model with Descriminative prior
"""
def __init__(self, Y, in... | mikecroucher/GPy | GPy/models/dpgplvm.py | Python | bsd-3-clause | 1,046 | [
"Gaussian"
] | 5c4c4e72f7fa63a9f1fe6e1c05dd2266bbaeb4a40c1107c1d9ba2b5b1f62fb80 |
#
# File : keil.py
# This file is part of RT-Thread RTOS
# COPYRIGHT (C) 2006 - 2015, RT-Thread Development Team
#
# 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... | weiyuliang/rt-thread | tools/cdk.py | Python | apache-2.0 | 4,091 | [
"CDK"
] | 81fcfea3545077bea7893635b6163f78d67a535c4c2570410a01dbcb87ae6fdd |
import logging
import os
import shutil
import galaxy.tools
from galaxy import util
from galaxy.datatypes import checkers
from galaxy.tools import parameters
from galaxy.util.expressions import ExpressionContext
from galaxy.web.form_builder import SelectField
from galaxy.tools.actions.upload import UploadToolAction
fr... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/tool_shed/util/tool_util.py | Python | gpl-3.0 | 12,468 | [
"Galaxy"
] | 2292a71b90d7e166596bdfaff66aa1935b8bee22281576f90b9c9b0a7e3e7ba2 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
#******************************************************************************
# ZYNTHIAN PROJECT: Zynthian GUI
#
# Zynthian GUI Step-Sequencer Class
#
# Copyright (C) 2015-2020 Fernando Moyano <jofemodo@zynthian.org>
# Copyright (C) 2015-2020 Brian Walton <brian@riban.co.uk>... | zynthian/zynthian-ui | zyngui/zynthian_gui_patterneditor.py | Python | gpl-3.0 | 40,318 | [
"Brian"
] | 4c045a93b20811c5aac5276d78fcc6dcc37e9ba500747581cbf39d34242cbad2 |
import numpy as np
try:
from scipy import constants
C_LIGHT = constants.c/1000.0
except TypeError: # This can happen during documentation builds.
C_LIGHT = 299792458.0/1000.0
# code to make mock Lya spectra following McDonald et al. (2006)
# copied from c++ code in Cosmology/LNLyaF
def power_amplitude(z)... | desihub/desisim | py/desisim/lya_mock_p1d.py | Python | bsd-3-clause | 5,006 | [
"Gaussian"
] | 37d2eeb0e4acafdf82fe35292e42287564a152f05c6e0ba5d264f377068108aa |
#!/usr/bin/env python2.7
# -*- coding: utf-8 -*-
####################################################################################
### Copyright (C) 2015-2019 by ABLIFE
####################################################################################
########################################################... | ablifedev/ABLIRC | ABLIRC/bin/public/iv_cluster/get_CTSS.py | Python | mit | 10,604 | [
"HTSeq"
] | 45fed5b6f78ce9fcbf258b7d53892ca4d977be9ce26605ce2186e5f6d567517b |
# 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... | sleuthkit/autopsy | pythonExamples/Aug2015DataSourceTutorial/FindContactsDb_v2.py | Python | apache-2.0 | 8,495 | [
"Brian"
] | 3dcca3457c4eab8fe17ed241fd41b911fa6c324381a3c3cb98a697e349ed81d2 |
"""
Trim GTFS feeds according to user input.
"""
import csv
import curses
import functools
import logging
import operator
import os
import sys
import typing
import zipfile
from . import chooser
from . import gtfs
logger = logging.getLogger(__name__)
ROUTE_TYPES_FILENAME: str = os.path.join(
os.path.dirname(__fi... | ben-e-whitney/next-train | next_train/wizard.py | Python | gpl-3.0 | 8,373 | [
"VisIt"
] | 85536cf5cbd58365e6a6bb04138be7443b1bfe1276ceaa260a4a9c9f4c874445 |
#! /usr/bin/env python
# MMapArea.py
# This file is part of Labyrinth
#
# Copyright (C) 2006 - Don Scorgie <Don@Scorgie.org>
#
# Labyrinth 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 th... | cristian99garcia/laybrinth-activity | src/MMapArea.py | Python | gpl-2.0 | 53,597 | [
"FLEUR"
] | 447b283eb187133f6a5b5eb21e3402c8561ad210be5cce4c376c734d17f76356 |
#!/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... | protonn/Electrum-Cash | plugins/trustedcoin/qt.py | Python | mit | 10,704 | [
"VisIt"
] | e71e7e5a216f727e05dac6aaf1002332940f9bc34b11b36b312e890cef9230f7 |
"""
Connects to the Galaxy Eggs distribution site and downloads any eggs needed.
If eggs for your platform are unavailable, fetch_eggs.py will direct you to run
scramble.py.
"""
import os, sys, logging
from optparse import OptionParser
parser = OptionParser()
parser.add_option( '-c', '--config', dest='config', help=... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/scripts/fetch_eggs.py | Python | gpl-3.0 | 2,732 | [
"Galaxy"
] | c484f83b19d13e380d7db8cb7083bc86cadba47df5fdf7222c1c963b23341081 |
#!/usr/bin/env python
###############################################################################
# Copyright (C) 1994 - 2004, Performance Dynamics Company #
# #
# This software is licensed as described in the file ... | peterlharding/PDQ | examples/misc/jackpdq.py | Python | mit | 4,760 | [
"VisIt"
] | 80ddbc28c06937adef82e36145acf8359208604a50ca51d43c1105f474b4ad87 |
# -*- coding: utf-8 -*-
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import SchemaMigration
from django.db import models
class Migration(SchemaMigration):
def forwards(self, orm):
# Adding field 'Visit.survey_sent'
db.add_column(u'clinics_visit', 'surve... | myvoice-nigeria/myvoice | myvoice/clinics/migrations/0017_auto__add_field_visit_survey_sent.py | Python | bsd-2-clause | 13,210 | [
"VisIt"
] | 46e236d9fac616f7808186ec093649151163b4e8c49491dbbede3d42d48768df |
#!/usr/bin/env python3
"""
This script is used to create a release of biocode for submission to PyPi.
Version numbering: This project uses a sequence-based (micro) scheme for
assigning version numbers:
http://the-hitchhikers-guide-to-packaging.readthedocs.io/en/latest/specification.html#sequence-based-scheme
... | jorvis/biocode | build/make_pypi_release.py | Python | mit | 9,328 | [
"BLAST"
] | 310b7935a423c4de34f1a026156e20cca4750d9b4a3908665e73c7081ecbee5d |
#!/usr/bin/env python
########################################################################
# $HeadURL$
########################################################################
__RCSID__ = "$Id$"
from DIRAC import exit as DIRACExit
from DIRAC.Core.Base import Script
if __name__ == "__main__":
Script.... | Sbalbp/DIRAC | DataManagementSystem/scripts/dirac-dms-remove-replicas.py | Python | gpl-3.0 | 1,803 | [
"DIRAC"
] | 5d5d4cf863252b4ff4a0c4fa077c0f957c653d7e3ed1eadd75df7aac73cc7199 |
#!/usr/bin/env python
"""
This script generates API changes between two different versions of VTK.
The script uses git and ctags to preset a list of classes added/removed, public
methods added/removed when going from one version to the other.
"""
# ctags generated by the command:
# ctags -R --sort=yes --c++-kinds=cf --... | hendradarwin/VTK | Utilities/Maintenance/semanticDiffVersion.py | Python | bsd-3-clause | 20,571 | [
"VTK"
] | 8bd385da149f6c36394ed24876a80376e0fbb5576314e613cb6b83e98a0afb40 |
# Copyright (C) 2009 by Eric Talevich (eric.talevich@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.
"""Utilities for handling, displaying and exporting Phylo trees.
Third-party libraries ... | poojavade/Genomics_Docker | Dockerfiles/gedlab-khmer-filter-abund/pymodules/python2.7/lib/python/Bio/Phylo/_utils.py | Python | apache-2.0 | 20,833 | [
"Biopython"
] | 6a22bd6933d5a87f99d0d4faf654baf686a68cecef561f91c27e06e7ea63b85e |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors: Kyle A. Beauchamp
#
# MDTraj i... | daviddesancho/mdtraj | mdtraj/geometry/__init__.py | Python | lgpl-2.1 | 2,293 | [
"MDTraj"
] | f4559801e9d46864424b6ac76b38a2f2f31946a2e32a1843b9a1a873860a8859 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import numpy as np
from pymatgen.core.structure import Structure
from pymatgen.util.coord_utils import get_linear_interpolated_value
from monty.json import MSO... | xhqu1981/pymatgen | pymatgen/phonon/dos.py | Python | mit | 5,900 | [
"Gaussian",
"pymatgen"
] | 562a6b7025f8d000915b471a0e225661637567a2c6ce569d54ff0ebed20713e8 |
# TODO: to be moved to TestDIRAC and transformed into a real test
########################################################################
# File: ReplicateAndRegisterTests.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/05/13 18:38:55
########################################################################
"... | sposs/DIRAC | DataManagementSystem/test/IntegrationFCT.py | Python | gpl-3.0 | 6,261 | [
"DIRAC"
] | 1a9fc9f73154f4eace182773634ead60e7e710223a314ad58c759a655ed50072 |
#!/usr/bin/env python
# coding: utf-8
import librosa
import logging
import numpy as np
from scipy.spatial import distance
from scipy import signal
from scipy.ndimage import filters
from msaf.algorithms.interface import SegmenterInterface
import msaf.utils as U
def median_filter(X, M=8):
"""Median filter along th... | urinieto/msaf | msaf/algorithms/sf/segmenter.py | Python | mit | 7,008 | [
"Gaussian"
] | d6ed1f3b7b806d74b55a71536a27844f392a953b0732af18291da6d345bbe857 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2022 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | psi4/psi4 | tests/runtest.py | Python | lgpl-3.0 | 5,306 | [
"Psi4"
] | 61c8b3d3c9705082e7d4c0cbcb96761137f07c371cbfe348042cdba155026c48 |
# Copyright (C) 2014-2016 Codethink Limited
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; version 2 of the License.
#
# This program is distributed in the hope that it will be useful,
# but... | perryl/morph | morphlib/sourceresolver.py | Python | gpl-2.0 | 22,183 | [
"VisIt"
] | 1b75312c4424f274a76973ef7ea670706a76714b588cec54e1232eb670147132 |
""" Tests generating files for qm torsion scan """
import unittest
from torsionfit.tests.utils import get_fun, has_openeye
import torsionfit.qmscan.torsion_scan as qmscan
import tempfile
import os
from fnmatch import fnmatch
import shutil
class TestQmscan(unittest.TestCase):
@unittest.skipUnless(has_openeye, 'C... | ChayaSt/Torsions | torsionfit/tests/test_qmscan.py | Python | gpl-2.0 | 1,512 | [
"Psi4"
] | d68a29377e021d064f42b95e52a41d84d763274d7879dda3631c371d34c15f56 |
#!/people/thnfs/homes/wehnerj/python-virtual/bin/python
import MDAnalysis as MD
import MDAnalysis.core.log as MDlog
import collections as col
#from MDAnalysis.core.parallel.distances import distance_array
import numpy as np
from MDAnalysis.core.distances import distance_array
from MDAnalysis.core.util import normal,ang... | 12AngryMen/votca-scripts | Gromacs/ordertrans_new.py | Python | apache-2.0 | 6,150 | [
"MDAnalysis"
] | f6b9a0359253b873c4d3a7b83363f23c4862e12320058838c1cfda6ac992d0a5 |
############################################
# [config.py]
# CONFIGURATION SETTINGS FOR PROSODIC
#
# Here you may change the runtime settings for prosodic.
# For more help on this file, please see the README in this folder,
# or visit it online: <https://github.com/quadrismegistus/prosodic>.
# If you have any questions... | kaysinds/PoopDog | config_backup.py | Python | gpl-3.0 | 14,244 | [
"VisIt"
] | d5a7022d39d67f654318650eff53d8a40b158658c62ab0a9fc5ffda8403f0b66 |
# hg.py - hg backend for convert extension
#
# Copyright 2005-2009 Matt Mackall <mpm@selenic.com> and others
#
# This software may be used and distributed according to the terms of the
# GNU General Public License version 2 or any later version.
# Notes for hg->hg conversion:
#
# * Old versions of Mercurial didn't tr... | seewindcn/tortoisehg | src/hgext/convert/hg.py | Python | gpl-2.0 | 23,506 | [
"Octopus"
] | 07d48ab69061b16f92bfb18dad123e60959c59ff3d80b84c0607151bfdc0a64d |
# coding: utf-8
# Copyright (c) Henniggroup.
# Distributed under the terms of the MIT License.
from __future__ import division, print_function, unicode_literals, \
absolute_import
""" use the interface module to create bare slab """
from pymatgen.core.structure import Structure
from pymatgen.io.vasp.inputs impor... | henniggroup/MPInterfaces | examples/create_slab.py | Python | mit | 1,117 | [
"ASE",
"VASP",
"pymatgen"
] | a1747a6936cf46651b0d309473a432ccf954636d5f6838ed53b4081e7f6e939a |
# 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 PyGetorganelle(PythonPackage):
"""Organelle Genome Assembly Toolkit (Chloroplast/Mitocondr... | LLNL/spack | var/spack/repos/builtin/packages/py-getorganelle/package.py | Python | lgpl-2.1 | 1,252 | [
"BLAST"
] | 5205ecc6e948fb45d7dbfafbb9a53a38d8fee4b9b025d93c54cb2a4a4b7584fa |
# Copyright 2020 Tensorforce Team. 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 la... | reinforceio/tensorforce | tensorforce/agents/dqn.py | Python | apache-2.0 | 12,802 | [
"Gaussian"
] | 727194e8c9db9f7aa7b9f2d4797d2579e4b292f6be29f69c040247d71498c89e |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# A script to test the mask filter.
# replaces a circle with a color
# Image pipeline
reader = vtk.vtkPNMReader()
reader.ReleaseDataFlagOff()
reader.SetFileName("" + str(VTK_DATA_ROO... | HopeFOAM/HopeFOAM | ThirdParty-0.1/ParaView-5.0.1/VTK/Imaging/Core/Testing/Python/TestMask2.py | Python | gpl-3.0 | 1,722 | [
"VTK"
] | e75a04c15ea00c59834e139f53fe51a3a196d376c14454eb865aedcf5c78d7ca |
# Copyright (c) 2001-2014, Canal TP and/or its affiliates. All rights reserved.
#
# This file is part of Navitia,
# the software to build cool stuff with public transport.
#
# Hope you'll enjoy and contribute to this project,
# powered by Canal TP (www.canaltp.fr).
# Help us simplify mobility and open public tr... | prhod/navitia | source/jormungandr/jormungandr/utils.py | Python | agpl-3.0 | 7,289 | [
"VisIt"
] | 55910cc438e4d04f87519ce10af5dc92466dedb1978f4d0d9d6b2e7e05645ecb |
from dateutil.relativedelta import relativedelta
from edc_visit_schedule import VisitSchedule, Schedule, Visit
from edc_visit_schedule import FormsCollection, Crf, Requisition
from edc_visit_schedule.visit.requisition import Panel as BasePanel
app_label = 'edc_metadata'
class Panel(BasePanel):
def __init__(sel... | botswana-harvard/edc-entry | edc_metadata/tests/visit_schedule.py | Python | gpl-2.0 | 3,940 | [
"VisIt"
] | bbe45af470759f64aebfd3290656a8261ff1990791377f233bb19ba590879c3a |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This package implements modules for input and output to and from VASP. It
imports the key classes form both vasp_input and vasp_output to allow most
classes to be simply called as pymatgen.io.vasp.Incar fo... | gVallverdu/pymatgen | pymatgen/io/vasp/__init__.py | Python | mit | 603 | [
"VASP",
"pymatgen"
] | 7f518c4d013f83921e016148bbf04b5d9d62e5da1493a749f010065d51199653 |
"""
The :mod:`sklearn.covariance` module includes methods and algorithms to
robustly estimate the covariance of features given a set of points. The
precision matrix defined as the inverse of the covariance is also estimated.
Covariance estimation is closely related to the theory of Gaussian Graphical
Models.
"""
from ... | glemaitre/scikit-learn | sklearn/covariance/__init__.py | Python | bsd-3-clause | 1,309 | [
"Gaussian"
] | d1e62db96312b9537006402cdbb574012e9fb4c40f33315b33de6f7ea292ebc1 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# File: InfoGAN-mnist.py
# Author: Yuxin Wu
import cv2
import numpy as np
import tensorflow as tf
import os
import argparse
from tensorpack import *
from tensorpack.utils import viz
from tensorpack.tfutils.scope_utils import auto_reuse_variable_scope, under_name_scope
fr... | eyaler/tensorpack | examples/GAN/InfoGAN-mnist.py | Python | apache-2.0 | 10,728 | [
"Gaussian"
] | 31fc32352df5ab4bdab17cd48597aa78733e605fdabd3347254a99aaf77585e5 |
import sys
from PyFastBDT import FastBDT
from PyFastBDT import utility
import numpy as np
import numpy
import numpy.linalg
import sklearn.metrics
import matplotlib.pyplot as plt
import matplotlib as mpl
def calculate_cdf_and_pdf(X):
"""
Calculates cdf and pdf of given sample and adds under/overflow bins
... | thomaskeck/FastBDT | examples/ugboost.py | Python | gpl-3.0 | 4,224 | [
"Gaussian"
] | 3137b1219cea5086d41c71d9e876702b7fb266c08f90c5f6755d62ec7aeb16dc |
import pandas as pd
import time
import numpy as np
import json
import simplejson
import urllib
import config
import ast
import bs4
import geocoder
from helpers import *
from math import cos, radians
import us_state_abbrevation as abb
from bs4 import BeautifulSoup as BS
from pymongo import MongoClient
import re
client ... | kennethcc2005/travel_with_friends | web_scraping_tripadvisor.py | Python | mit | 13,608 | [
"VisIt"
] | 45c92a96f500b6d8524ac4175d9cd66928cf8618d568a7d7cb72319e92a8ec2c |
#
# Quru Image Server
#
# Document: tests.py
# Date started: 05 Apr 2011
# By: Matt Fozard
# Purpose: Contains the image server development test suite
# Requires:
# Copyright: Quru Ltd (www.quru.com)
# Licence:
#
# This program is free software: you can redistribute it and/or modify
# it ... | quru/qis | src/tests/tests.py | Python | agpl-3.0 | 123,814 | [
"Galaxy"
] | b6e2346384c48c190053fd74d6353e68bc958083c991d568b803c137835d9505 |
##############################################################################
# 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... | lgarren/spack | var/spack/repos/builtin/packages/r-agdex/package.py | Python | lgpl-2.1 | 1,774 | [
"Bioconductor"
] | d005eeb93d1a2c9468e5a21a9b8e79ce67ad182f93c8e87d2df669bb6656e1f6 |
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