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"""
How to reference supporting evidence for some object in the database.
See: "Metadata in PyOpenWorm" for discussion on semantics of what giving
evidence for an object means.
"""
import sys
import PyOpenWorm as P
#Create dummy database configuration.
d = P.Data({})
#Connect to database with dummy configuration
P.... | hnunner/PyOpenWorm | examples/add_reference.py | Python | mit | 1,042 | [
"NEURON"
] | dfe5c57973b5cc94e660e35784ecc90c5ea80c30d7f5a172cec830ade780aa4f |
"""
This script is used to design the design matrix for our linear regression.
We explore the influence of linear and quadratic drifts on the model
performance.
Script for the raw data.
Run with:
python noise-pca_script.py
from this directory
"""
from __future__ import print_function, division
import sys, os,... | timothy1191xa/project-epsilon-1 | code/utils/scripts/noise-pca_script.py | Python | bsd-3-clause | 13,899 | [
"Gaussian"
] | f7059fde41be59156ca52cba878ecc3d196570e71bf349934939500c1ec34fec |
../../../../share/pyshared/orca/mag.py | Alberto-Beralix/Beralix | i386-squashfs-root/usr/lib/python2.7/dist-packages/orca/mag.py | Python | gpl-3.0 | 38 | [
"ORCA"
] | f0856452354d553cd495e95bd5171f6059689dec7c5b5615a1bdddb6f097869f |
from __future__ import print_function
import numpy as np
LA = np.linalg
import cv2
from scipy.sparse import linalg as spla
import vtk
from util import kinect, format
def genPoints(ptArray):
points = vtk.vtkPoints()
points.SetNumberOfPoints(len(ptArray))
for i in range(len(ptArray)):
poi... | FYP-DES5/deepscan-core | core.py | Python | mit | 7,630 | [
"VTK"
] | 321acadb347f11d8890ab6bafa7ce29c28a4a64fd6cdd034863594cf34060af7 |
# -*- coding: utf-8 -*-
{
"'Sounds-like' name search allowing search even the spelling of the name is not known exactly": "'Sounds-like'名稱搜尋或搜尋,即使名稱的拼字不完全",
"A location that specifies the geographic area for this region. This can be a location from the location hierarchy, or a 'group location', or a location that ha... | collective/eden | languages/zh-tw.py | Python | mit | 338,517 | [
"VisIt"
] | 085ce55dbb5d267c28049b24a45c8381f2ce3877d334b4c518ffaa681116f5f6 |
#!/usr/bin/env python
'''
Computing nuclear spin-spin coupling constants
'''
from pyscf import gto, scf, dft
from pyscf.prop import ssc
mol = gto.M(atom='''
O 0 0 0
H 0 -0.757 0.587
H 0 0.757 0.587''',
basis='ccpvdz')
mf = scf.UHF(mol).run()
ssc.UHF(mf).kernel()
... | gkc1000/pyscf | examples/prop/05-ssc.py | Python | apache-2.0 | 383 | [
"PySCF"
] | db83655796b2e82cda83d0ef449b60aa343fe8af718ee78b4fddd5dc921cd4e7 |
import matplotlib.pyplot as plt
import os
from astropy.table import Table
# setup information sources
degas = Table.read(os.path.join(os.environ['SCRIPTDIR'],'degas_base.fits'))
stack = Table.read('/lustre/cv/users/akepley/degas/stack_test/stack_IR6p0_mom1.fits')
plotDir = os.path.join(os.environ['ANALYSISDIR'],'plo... | low-sky/degas | scripts/plot_SFEdense_vs_mstar.py | Python | gpl-3.0 | 1,650 | [
"Galaxy"
] | aba7a1ad7340336315338199646f75b15c29b19059fbafafbeaa808352ffaec4 |
from bs4 import BeautifulSoup, SoupStrainer
import os.path
import re
import time
import urllib2
import webbrowser
import whoisclient
import wx
import xlrd
class Panel_Criteria(wx.Panel):
""" Panel_Criteria() is the wx.Panel where the criteria and innocuous criteria that will be checked for are set.
"""
d... | shannonturner/scam-scanner | ScamScanner.py | Python | mit | 72,737 | [
"VisIt"
] | c1e9e0d1ba0a94748be67bf4c698d57634684851c3f6a1805d0ee814d853d645 |
from __future__ import annotations
from dials.algorithms.refinement.parameterisation.prediction_parameters import (
PredictionParameterisation,
SparseGradientVectorMixin,
)
from dials.array_family import flex
from dials_refinement_helpers_ext import dRq_de
class StillsPredictionParameterisation(PredictionPar... | dials/dials | algorithms/refinement/parameterisation/prediction_parameters_stills.py | Python | bsd-3-clause | 18,168 | [
"CRYSTAL"
] | 823468f6a758a140d363d632043bfd334bceaba2f475bca35fb9fa11a5dcba44 |
# -*- coding: utf-8 -*-
# Advanced Emulator Launcher miscellaneous functions
# Copyright (c) 2016-2019 Wintermute0110 <wintermute0110@gmail.com>
# Portions (c) 2010-2015 Angelscry and others
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License... | chrisism/plugin.program.advanced.emulator.launcher | resources/utils.py | Python | gpl-2.0 | 101,421 | [
"Jaguar"
] | 1b44e4b2963e54c177e59c7e3493f8388f77596e2a5768622b5f9a43dac71de9 |
'''
Base class from which PyNoddy experiments should inherit.
Much basic functionality (random perturbation, plotting etc. is defined here).
Thought: perhaps drawing functions etc. should be moved into NoddyOutput class?
@author: flohorovicic, samthiele
'''
import os
import numpy as np
<<<<<<< HEAD
from pynoddy.hi... | Leguark/pynoddy | pynoddy/experiment/__init__.py | Python | gpl-2.0 | 28,534 | [
"ParaView",
"VTK"
] | d27bbab0870cd3fb46d14c8f46c10369644af14c07d0df2d60129cbacbbceb5a |
from __future__ import annotations
import logging
import random
import sys
import numpy as np
import iotbx.phil
from dials.array_family import flex
from dials.util.exclude_images import exclude_image_ranges_for_scaling
from dials.util.multi_dataset_handling import (
assign_unique_identifiers,
parse_multiple_... | xia2/xia2 | src/xia2/cli/multiplex.py | Python | bsd-3-clause | 5,241 | [
"CRYSTAL"
] | cdce6634af35d812498ef4e053028fd3c73f75351b3cd6bbc8e82adb6fb5581c |
# This file is part of cclib (http://cclib.github.io), a library for parsing
# and interpreting the results of computational chemistry packages.
#
# Copyright (C) 2006-2014, the cclib development team
#
# The library is free software, distributed under the terms of
# the GNU Lesser General Public version 2.1 or later. ... | Clyde-fare/cclib | src/cclib/method/fragments.py | Python | lgpl-2.1 | 5,744 | [
"ADF",
"cclib"
] | f0a8e583ac3057dc452bfda573a0443854811dbd58a53f2db49bf51f890b12f7 |
"""
This file contains functions for the generation of random
quaternions using various statistical distributions (namely
uniform and gaussian).
It is also useful simply for generating random axes.
"""
import pyquat as pq
from math import sqrt, cos, sin, pi
import numpy as np
def randu(symmetric_range = 1.0):
"... | mohawkjohn/pyquat | pyquat/random.py | Python | bsd-3-clause | 1,849 | [
"Gaussian"
] | 7335dc625b1b808a55de2221c00501341db85cf9b37ba2bda02e2eb28f89050c |
# Copyright 2014-2017 CERN. This software is distributed under the
# terms of the GNU General Public Licence version 3 (GPL Version 3),
# copied verbatim in the file LICENCE.md.
# In applying this licence, CERN does not waive the privileges and immunities
# granted to it by virtue of its status as an Intergovernmental... | blond-admin/BLonD | __EXAMPLES/main_files/EX_01_Acceleration.py | Python | gpl-3.0 | 4,706 | [
"Gaussian"
] | 4d69a8c70646da7c8eed4d6ca12e01c14cc29d8dfa117951a40aa31fd5048c02 |
"""
{description}
Copyright (C) {2014} {Karl Parkinson}
This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.
... | KarlParkinson/Graphs | AlgorithmHandler.py | Python | gpl-2.0 | 6,230 | [
"VisIt"
] | d0d2dd133cfae9d5ae6dbd88b26c5b9bce7ebb6dbdf43de5023c4d1d65928921 |
# -*- coding: utf-8 -*-
"""
pyap.source_US.data
~~~~~~~~~~~~~~~~~~~~
This module provides regular expression definitions required for
detecting Canada addresses.
The module is expected to always contain 'full_address' variable containing
all address parsing definitions.
:copyright: (c) 2... | vladimarius/pyap | pyap/source_CA/data.py | Python | mit | 21,646 | [
"ASE"
] | 08a06ba89fe59f7951f571878a912aabc131567947b97baa6c300e744589d220 |
# -*- coding: utf-8 -*-
# Unit tests for cache framework
# Uses whatever cache backend is set in the test settings file.
from __future__ import unicode_literals
import copy
import io
import os
import re
import shutil
import tempfile
import threading
import time
import unittest
import warnings
from django.conf import... | loic/django | tests/cache/tests.py | Python | bsd-3-clause | 87,274 | [
"Brian"
] | e24ceb11adebf8368c3e8cbb34527753a42fc2e3450afe986659e313b53f3395 |
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import unittest
import pytest
from monty.serialization import loadfn
from pymatgen.analysis.bond_dissociation import BondDissociationEnergies
module_dir = os.path.join(os.path.dirname(os.path.abspath(__file__)))
... | vorwerkc/pymatgen | pymatgen/analysis/tests/test_bond_dissociation.py | Python | mit | 15,432 | [
"pymatgen"
] | 14602f52a147aa3bed3edb94555c1b6d7a68c5425e42a11b345e64b36b897481 |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publi... | thica/ORCA-Remote | src/ORCA/widgets/core/SliderEx.py | Python | gpl-3.0 | 5,982 | [
"ORCA"
] | 6a1c9d6703ec49c5fbfb96d183c95a552a21b3862ebf87ae1b1aba602e4d8cc0 |
#!/usr/bin/env python
import click
import sys
import json
from datetime import datetime
import os
import threading
import time
from random import random
sys.path.append("libs");
from log import log
import logging
import worker
class Config(object):
def __init(self):
self.debug = False
pass_config = clic... | librae8226/flats | flats.py | Python | mit | 5,500 | [
"Gaussian"
] | 413f8bca43da6083198d9fa778bdcc77f8fef95dd8ca6cfe4eb9f2ef4a91803a |
from ase.utils.sphinx import mol_role
from ase.utils.sphinx import svn_role_tmpl, trac_role_tmpl, epydoc_role_tmpl
from ase.utils.sphinx import create_png_files
def svn_role(role, rawtext, text, lineno, inliner, options={}, content=[]):
return svn_role_tmpl('http://svn.fysik.dtu.dk/projects/'
... | grhawk/ASE | tools/doc/ext.py | Python | gpl-2.0 | 1,249 | [
"ASE"
] | b58a574bd9eda4dd4c0ce80f9b3e3e7cd2c9efa01da77714f5c361f6e6bc6fcf |
# -*- python -*-
#
# This file is part of cellnopt software
#
# Copyright (c) 2014 - EBI-EMBL
#
# File author(s): Thomas Cokelaer <cokelaer@ebi.ac.uk>
#
# Distributed under the GPLv3 License.
# See accompanying file LICENSE.txt or copy at
# http://www.gnu.org/licenses/gpl-3.0.html
#
# website: http://github.... | cellnopt/cellnopt | cno/feeder/feeder.py | Python | bsd-2-clause | 4,345 | [
"Bioconductor"
] | 8b133a0e1e853666ceed7f40b37c5eee77a24fc9658a53291f18dbe5dcf857b4 |
import kivy
kivy.require('1.8.0')
from kivy.app import App
from kivy.properties import ObjectProperty
from kivy.uix.boxlayout import BoxLayout
from kivy.uix.popup import Popup
from kivy.clock import Clock
from plyer import accelerometer
'''
This example uses Kivy Garden Graph addon to draw graphs plotting the
acce... | inclement/plyer | examples/accelerometer/using_graph/main.py | Python | mit | 2,732 | [
"VisIt"
] | 24b52a35a1fbd357179e411e3c68ffd73673a7680fe46af063480acbf17c6d83 |
# -*- coding: utf-8 -*-
# Copyright (c) 2013-2014 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2013-2014 Google, Inc.
# Copyright (c) 2014-2018 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2014 Cosmin Poieana <cmin@ropython.org>
# Copyright (c) 2014 Vlad Temian <vladtemian@gmail.com>
# Copy... | ekwoodrich/python-dvrip | env/lib/python3.5/site-packages/pylint/checkers/stdlib.py | Python | mit | 16,541 | [
"VisIt"
] | 5db1e236925161aae4c4021718c3f16d170330363748bd5b831b84028c1ef075 |
# 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 print_function
import ast
import gyp.common
import gyp.simple_copy
import multiprocessing
import optparse
import os.path
import re
import ... | enclose-io/compiler | lts/tools/gyp/pylib/gyp/input.py | Python | mit | 116,891 | [
"VisIt"
] | aebe31bc5508a89d930307b370e72e299af2a21d5a0d6f75ad166e8484479262 |
ARTEMIS_SYMBOLS = {
"$17": "0017",
"$3": "0003",
"$4": "0004",
"$5": "0005",
"$6": "0006",
"$7": "0007",
"'": "13,2570",
"*NBSM*": "23,3647",
"*SMNB*": "23,3633",
"+2ACTDEG": "20,2462",
"+DECSGN": "40,2203",
"+DOWN": "00,2607",
"+LIMIT": "42,3246",
"+MGA": "E7,162... | jimlawton/pyagc-googlecode | agcasm/artemis072_symbols.py | Python | gpl-2.0 | 185,375 | [
"BLAST"
] | 09bd08fe4c49c0899b8c72f5f548f04e7d3c170269adf163ea1185ab08ad03ee |
# Copyright: (c) 2019, 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
import fnmatch
import json
import operator
import os
import shutil
import sys
import tarfile
impor... | sestrella/ansible | lib/ansible/galaxy/collection.py | Python | gpl-3.0 | 39,560 | [
"Galaxy"
] | 2d6e306e0bf3bc8dd7f02c27bfbed905fa140a5f6f7244da004e53d2e7f65fc9 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- http://www.mdanalysis.org
# Copyright (c) 2006-2016 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#
... | kain88-de/mdanalysis | testsuite/MDAnalysisTests/analysis/test_encore.py | Python | gpl-2.0 | 38,962 | [
"MDAnalysis"
] | a7d012c5d0af2e6d92642ffa7bf0e732f044ac60a4ccf6835da1872c0eb619de |
# Usage: a collection of cosmology and cluster tools
# cosmoparams should be of the form:
# cosmoparams = {'OmegaM':0.3121,'OmegaL':0.6879,'Omegak':0.,'hubble':0.6751}
# assumes the following import statements:
# import numpy as np
G = 4.3016e-9 #Mpc/h km^2 (Msolar/h)^(-1) s^(-2)
###############... | maho3/gal-ML | old/cosmologyTools.py | Python | mit | 6,359 | [
"Galaxy"
] | cba7058aef15d017e2603060a0badfef46dfdfbda68999c851800abcb569a335 |
from pprint import pformat
import pytz
import os, sys, json, time, random, string
from functools import wraps
from datetime import datetime
import yaml
from collections import OrderedDict
from os.path import join
from more_itertools import unique_everseen
import logging
from kids.cache import cache as cached
import tem... | elifesciences/builder | src/buildercore/utils.py | Python | mit | 12,429 | [
"VisIt"
] | 4788088d6e4f5c8e737bf2034d2540830304ce92c4740c20dfc4d7231f90602f |
"""
The 2-sphere, S^2
"""
import numpy as np
from numpy.polynomial.legendre import leggauss
def change_coordinates(coords, p_from='C', p_to='S'):
"""
Change Spherical to Cartesian coordinates and vice versa, for points x in S^2.
In the spherical system, we have coordinates beta and alpha,
where beta ... | AMLab-Amsterdam/lie_learn | lie_learn/spaces/S2.py | Python | mit | 13,852 | [
"Mayavi"
] | 5cf7506e7cea466c116a0e39710cae6d7ce63846a6db31c5afdb95dcc5b3d7e0 |
# -*- coding: utf-8 -*-
"""
Acceptance tests for Video.
"""
import os
from unittest import skipIf
from ddt import data, ddt, unpack
from mock import patch
from nose.plugins.attrib import attr
from selenium.webdriver.common.action_chains import ActionChains
from selenium.webdriver.common.by import By
from common.test... | Lektorium-LLC/edx-platform | common/test/acceptance/tests/video/test_video_module.py | Python | agpl-3.0 | 55,244 | [
"VisIt"
] | 5b378186b1fe96a0f2bc924933373139ed705b0fe6ab76e4258b30a618f7af60 |
#!/usr/bin/env python
#Dan Blankenberg
"""
Takes a Multiple Alignment FASTA file and concatenates
sequences for each species, resulting in one sequence
alignment per species.
"""
import sys, tempfile
from galaxy import eggs
from galaxy.tools.util.maf_utilities import iter_fasta_alignment
from galaxy.util.odict impor... | xibalbanus/PIA2 | osiris_phylogenetics/alignment/fasta_concatenate_by_species.py | Python | mit | 1,380 | [
"Galaxy"
] | cc5a1e6aa9052c2738316fcccf729b6d16aa936f7114edd43cad82c807327523 |
#!/usr/bin/python
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# Ansible is distributed... | dav1x/ansible | lib/ansible/modules/cloud/amazon/ec2_elb_lb.py | Python | gpl-3.0 | 53,260 | [
"Dalton"
] | a331924cfdb5ab15a176dfb1918f80839f1ac1400dbda17333ec63f998aec984 |
# -*- coding: utf-8 -*-
"""
This file is part of pyCMBS.
(c) 2012- Alexander Loew
For COPYING and LICENSE details, please refer to the LICENSE file
"""
import os
import sys
#~ from geoval.statistic import get_significance, ttest_ind
from pycmbs.netcdf import NetCDFHandler
import numpy as np
from matplotlib import ... | pygeo/pycmbs | pycmbs/data.py | Python | mit | 32,941 | [
"NetCDF"
] | eac4db6a9cf0e3df7664fc29ff92690c80a8a48f65215819d32d96d2f94eeec5 |
import os
from os.path import join
import numpy as n
def writeScript(rootName, plate):
f=open(rootName+".sh",'w')
f.write("#!/bin/bash \n")
f.write("#PBS -l walltime=260:00:00 \n")
f.write("#PBS -o "+plate+".o.$PBS_JOBID \n")
f.write("#PBS -e "+plate+".e$PBS_JOBID \n")
f.write("#PBS -M comparat@mpe.mpg.de \n")
f... | JohanComparat/pySU | spm/bin/write_run_scripts_dr7_chabrier.py | Python | cc0-1.0 | 961 | [
"Galaxy"
] | 0dc4ba8d1dfc28e00e6b583de0c98b4e69c85a2442f671f0144748eb35637ac5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Setup script for py2cytoscape
To install, run:
python setup.py install
"""
from setuptools import setup, find_packages
setup(
name='py2cytoscape',
version='0.5.0',
description='Utilities to use Cytoscape and Cytoscape.js from Python',
long_descrip... | scholer/py2cytoscape | setup.py | Python | mit | 1,600 | [
"Cytoscape"
] | 4e9f08a5b6381d1ee2a70c92623e56af04d516670e6dad4f63b0afd4199e9f22 |
# -*- coding: utf-8 -*-
from __future__ import print_function
"""
"""
__credits__ = ["Upi Lab"]
__author__ = "Aviral Goel"
__license__ = "GPL3"
__version__ = "1.0.0"
__maintainer__ = "Aviral Goel", "HarshaRani"
__email__ = "goel.aviral@gmail.com"
__status__ = "Development"
_... | BhallaLab/moose | moose-gui/PlotWidgetContainer.py | Python | gpl-3.0 | 5,811 | [
"MOOSE"
] | 91f9a7dd12be257b2d092846be1dbacf7ff9f8dd24d2970d5d80a78ff2ddf53e |
#!/usr/bin/env python -i
# preceeding line should have path for Python on your machine
# viz_vmd.py
# Purpose: viz running LAMMPS simulation via VMD
# Syntax: viz_vmd.py in.lammps Nfreq Nsteps
# in.lammps = LAMMPS input script
# Nfreq = dump and viz shapshot every this many steps
# Nsteps =... | sradl1981/LIGGGHTS-PUBLIC-ParScale | python/examples/viz_vmd.py | Python | gpl-2.0 | 2,063 | [
"LAMMPS",
"VMD"
] | 89b5caf5a3c7260fb046953db6f4f4c4c6148a8efad988acbb415695f5bdd4c3 |
################################################################################
# #
# Copyright (C) 2010-2018 The ESPResSo project #
# ... | mkuron/espresso | doc/tutorials/06-active_matter/EXERCISES/enhanced_diffusion.py | Python | gpl-3.0 | 5,085 | [
"ESPResSo"
] | 9947e57d4c16c8d4786e870c93270a502dad0c49a0c69b8d8824db6e970703c9 |
import logging
import lib.const as C
import lib.visit as v
from .. import util
from ..meta.template import Template
from ..meta.clazz import Clazz
from ..meta.method import Method
from ..meta.field import Field
from ..meta.statement import Statement, to_statements
from ..meta.expression import Expression
class Build... | plum-umd/pasket | pasket/rewrite/builder.py | Python | mit | 2,326 | [
"VisIt"
] | edc7a1633c49f0586d7b6a6e58bdf99785715c0932b188408f5f9f2431d0ae21 |
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# bu... | mathstuf/bodhi | bodhi/mail.py | Python | gpl-2.0 | 15,521 | [
"VisIt"
] | 1d4e19760802f472f81564c468c61623ed66a8ca6b869e1a93b9d8ee8b813e20 |
'''
This module contains all the stuff to make your way from python code to
a dynamic library, see __init__.py for exported interfaces.
'''
from pythran.backend import Cxx
from pythran.config import cfg, make_extension
from pythran.cxxgen import PythonModule, Define, Include, Line, Statement
from pythran.cxxgen import... | pbrunet/pythran | pythran/toolchain.py | Python | bsd-3-clause | 12,759 | [
"VisIt"
] | ed78a1487540f317929d2bd55d8c00ae7a1981ff0a6a66fcc33c7a1380f3864b |
# -*- coding: utf-8 -*-
"""
End-to-end tests for the Account Settings page.
"""
from datetime import datetime
from unittest import skip
import six
from bok_choy.page_object import XSS_INJECTION
from pytz import timezone, utc
from common.test.acceptance.pages.common.auto_auth import FULL_NAME, AutoAuthPage
from comm... | edx-solutions/edx-platform | common/test/acceptance/tests/lms/test_account_settings.py | Python | agpl-3.0 | 19,924 | [
"VisIt"
] | 69baf8c6a6edd30d43de30e54288cb64c4b07996db896ff3d6c4d9b52d4985ab |
def osc_sigmaExp(a,b,phi=0,T=24,A=10,llim=0,ulim=100,dx=0.1, r=15):
"""
Generate an oscillatory signal with withe gaussian noise around. The variance depend on x
Compute the signal:
y(x) = A sin(w t+ phi) +r +noise
w= 2 Pi/T (T is the period that you have to set in Kwargs)
noise is gaussian BUT ... | Repythory/Libraries | amolf/numerical_data_analysis/GenerateOsc.py | Python | bsd-2-clause | 2,608 | [
"Gaussian"
] | e83d97ad3d91e7aca3c83bedd535cf6721531cc2f359fbb210615cd24c34d628 |
#Script to rum Hmmer on Dicty Protiens
#Run it keeping in mind that HMM(s) from a particular DPM human holmolog protien are all checked against every Protien from Dicty
#Author : prakhar gaur
#date : Wed 16 July IST 2015
import os
import argparse
import csv
parser = argparse.ArgumentParser()
parser.add_argument('-C',... | gprakhar/scripts-biopython | hmmer-pipeline-DPM_Dicty.py | Python | gpl-3.0 | 1,173 | [
"BLAST"
] | 28a369bbbdc5d8b81b5c8fc6a0b6884b32f28cc901fc0b7a469e50e3f7478ad9 |
# 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 RSiggenes(RPackage):
"""Multiple Testing using SAM and Efron's Empirical Bayes Approaches.... | rspavel/spack | var/spack/repos/builtin/packages/r-siggenes/package.py | Python | lgpl-2.1 | 1,239 | [
"Bioconductor"
] | 5cdabfd5356e359e03cc20a2f71668ea20852e8a09ce772ea997f578e32d1820 |
import os
import sys
from glob import glob
import numpy as np
from astropy.io import fits
from scipy.linalg import lstsq
import scipy.ndimage as nd
from scipy import optimize
class Grism():
"""Class to define parameters for the grism and create an object mask.
Defines pathnames, filesnames, appropriate flats... | HSTWISP/WISPIPE | PYTHON/fit_multi_sky.py | Python | gpl-3.0 | 19,188 | [
"Gaussian"
] | 9fd91a619e62c36c30cc9c6d64036c5165290eb7aa343cb12caf33def2ea13a9 |
'''
Inspired by the LHCbDIRAC ModuleBase class
Created on Feb 6, 2014
@author: stephanep
'''
from DIRAC import gLogger, S_OK, S_ERROR
from DIRAC.Core.Security.ProxyInfo import getProxyInfoAsString
from DIRAC.ConfigurationSystem.Client.Helpers.Opera... | sposs/DIRACInterfaceDoc | code/Workflow/Modules/ModuleBase.py | Python | gpl-2.0 | 22,715 | [
"DIRAC"
] | aa8ff6ef6c6a40a05d3f6cb204159bc14c0c620fa5bc9d69b0da86b9ee25c107 |
# usage: cat pysam_ex1.bam | python pysam_test_stdin.pyx
import pysam
samfile = pysam.Samfile( "-", "rb" )
# set up the modifying iterators
l = list(samfile.fetch( until_eof = True ))
assert len(l) == 3270
| pkaleta/pysam | tests/pysam_test_stdin.py | Python | mit | 210 | [
"pysam"
] | 16d9b163cd00c64bf211c8218c09079ffd641d8a4b109f30a7b2c4705bab65aa |
import argparse
import datetime
from collections import defaultdict
# from pgtools import toolbox
DEFAULT_CHROMOSOME_DIALECT = 'ensembl'
REPORTING_INTERVAL = 1000000
def convert_chroms(chrom_string, source, dest):
if source == dest:
return chrom_string
if source == 'ucsc':
if dest == 'ensemb... | phageghost/pg_tools | quarantine/bwtout_to_tagalign.py | Python | mit | 5,030 | [
"Bowtie"
] | 8f06e893c193688cbdc5fa73e34bb20a68aeb56cd31ff200dd9964a03756a442 |
# Copyright 2016 by Raytheon BBN Technologies Corp. All Rights Reserved.
"""
Check that the variable names referenced in a function are
defined within the scope of that function.
This is a useful heuristic in some cases, but is contrary
to the Python programming model, which permits this to be
more dynamic, using th... | BBN-Q/pyqgl2 | src/python/pyqgl2/scope.py | Python | apache-2.0 | 11,811 | [
"VisIt"
] | db2dea5425cbfe90e620fda1729595fd544eb3e72a781bb5835a4cfbc41020e1 |
#
# @file TestKineticLaw.py
# @brief SBML KineticLaw unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Ben Bornstein
#
# $Id$
# $HeadURL$
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by con... | alexholehouse/SBMLIntegrator | libsbml-5.0.0/src/bindings/python/test/sbml/TestKineticLaw.py | Python | gpl-3.0 | 8,284 | [
"VisIt"
] | 609c7ab542bc16f9832fcc281c58940e67dab12e971deb655b7df5bc21002fd2 |
__author__ = 'Thomas Rueckstiess, ruecksti@in.tum.de'
from pybrain.rl.learners.rllearner import RLLearner
from pybrain.utilities import abstractMethod
from pybrain.auxiliary import GradientDescent
from scipy import ravel
class PolicyGradientLearner(RLLearner):
""" The PolicyGradientLearner takes a ReinforcementDa... | daanwierstra/pybrain | pybrain/rl/learners/policygradients/policygradient.py | Python | bsd-3-clause | 1,908 | [
"Gaussian"
] | f5719c493075c8b11666be96eae79636e00a0c9f850c472ee4d14f7b686e6095 |
import os
import sys
import math
import argparse
import warnings
import numpy as np
from scipy.stats import uniform
path = os.path.normpath(os.path.join(os.path.dirname(sys.argv[0]), '..'))
sys.path.insert(0, path)
from uvmod import utils, models, stats, plotting
try:
import emcee
is_emcee = True
except ImportE... | ipashchenko/uvmod | bin/query_source.py | Python | mit | 13,697 | [
"Gaussian"
] | 3a86709a35f70df559fc0ed8025201a999d0782e0ec135b87185c41ac82e866d |
#!/usr/bin/env python
import sys
sys.path.append("../")
import numpy as np
import pandas as pd
import scipy.io
from functions import *
from sklearn.decomposition import PCA
import _pickle as cPickle
import neuroseries as nts
import sys
import scipy.ndimage.filters as filters
from sklearn.mixture import GaussianMixtu... | gviejo/ThalamusPhysio | python/figure_article/main_article_fig_1.py | Python | gpl-3.0 | 23,775 | [
"Gaussian",
"NEURON"
] | 7ff7858a72121824cb302731b5c496909f61a00ee4d2c8566fa93b980f7055e1 |
# This Source Code Form is subject to the terms of the Mozilla Public
# License, v. 2.0. If a copy of the MPL was not distributed with this file,
# You can obtain one at http://mozilla.org/MPL/2.0/.
from __future__ import print_function, unicode_literals
import os
import re
import subprocess
import sys
import tempfil... | Yukarumya/Yukarum-Redfoxes | python/mozboot/mozboot/osx.py | Python | mpl-2.0 | 23,552 | [
"VisIt"
] | 9daddf872cc0e4ac54e6c4c5e05e066e94ea99913b5d998ee59305d87b4daeb5 |
# Copyright 2016 Intel Corporation
#
# 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... | yidawang/brainiak | brainiak/utils/fmrisim.py | Python | apache-2.0 | 77,745 | [
"Gaussian"
] | d3e492cbf4cdf707ae4689973a498b3dd75ff8d045740cf6a0eea33616cf3e3c |
from common2 import *
# NAME IDEA -> pooling/random/sparse/distributed hebbian/horde/crowd/fragment/sample memory
# FEATURES:
# + boost -- neurons with empty mem slots learn faster
# + noise --
# + dropout -- temporal disabling of neurons
# + decay -- remove from mem
# + negatives -- learning to avoid detecting some... | mobarski/sandbox | rsm/v9le/v4.py | Python | mit | 5,658 | [
"NEURON"
] | ee84c04b971d3c887207acbecffc57c6b87c2037bdd416864165a543995f8e5f |
#
# @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 | psi4/driver/procrouting/response/__init__.py | Python | lgpl-3.0 | 968 | [
"Psi4"
] | 04c660f3e1a869ec7ac8865f1dc78e4804225e0557325e19b885a6277a630ea6 |
import ast
from ltdexec.dialect.base import Dialect
from ltdexec.processor.transform import TransformImportsAst
from ltdexec import exceptions
from .base import LtdExec_TestCaseBase
#==============================================================================#
class TransformImportsAst_TestCase(LtdExec_TestCaseBas... | dpwhite2/limitedexec | ltdexec/tests/test_transform.py | Python | bsd-2-clause | 2,766 | [
"VisIt"
] | 516ddd743998e2837dcdddc368277ed31060175bad471b35ed41e5131a0f5541 |
#!/usr/bin/env python
# Copyright (C) 2015 Adam Taranto <adam.p.taranto@gmail.com>
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any la... | Adamtaranto/frisk | setup.py | Python | gpl-3.0 | 2,103 | [
"pysam"
] | c146b027306ab66f4449a5b837ccc81d4b0b9b68db8f363b40d95c90025da098 |
#!/usr/bin/env python
#pylint: disable=missing-docstring
####################################################################################################
# DO NOT MODIFY THIS HEADER #
# MOOSE - Multiphysics Object Oriented Simu... | liuwenf/moose | python/MooseDocs/tests/bibtex/test_bibtex.py | Python | lgpl-2.1 | 3,812 | [
"MOOSE"
] | 7ec46cc61307855b8e9db11267358bdd99a69d29e1d4a4764b5200c7e086cfbb |
"""
Class and script for fitting microlensing model using MulensModel.
All the settings are read from a YAML file.
"""
import sys
from os import path, sep
import tempfile
import shutil
import warnings
import math
import numpy as np
from scipy.interpolate import interp1d
from matplotlib import pyplot as plt
from matplot... | rpoleski/MulensModel | examples/example_16/ulens_model_fit.py | Python | mit | 99,798 | [
"Gaussian"
] | 66f2b1c4af2d487285a829bbfc5ce4f587a1ae3c63b45099d4fc7b01812b15c5 |
# Copyright (c) 2012 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""Top-level presubmit script for Chromium.
See http://dev.chromium.org/developers/how-tos/depottools/presubmit-scripts
for more details about the presu... | TheTypoMaster/chromium-crosswalk | PRESUBMIT.py | Python | bsd-3-clause | 69,696 | [
"VisIt"
] | 6c1aefcf12e795aa5f680995401886a0c364a8f09763cffd8b28d51daf8a1dcf |
#!/usr/bin/env python
## category General
## desc Removes reads from a BAM file based on criteria
"""
Removes reads from a BAM file based on criteria
Given a BAM file, this script will only allow reads that meet filtering
criteria to be written to output. The output is another BAM file with the
reads not matching the ... | ngsutils/ngsutils | ngsutils/bam/filter.py | Python | bsd-3-clause | 28,175 | [
"pysam"
] | b1d9885bf07d5e0b897fbc873aecaaffb255841f3f9b2c907b6a0103226ab020 |
#!/usr/bin/env python
#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#-#
#
# Name: generate_gaussian_samples.py
#
# Author: Constantin Weisser (weisser@mit.edu)
#
# Purpose: This is a python script to write a file containing 10000 data points
# sampled from a 2D Gaussian
#
#-#-... | weissercn/MLTools | Dalitz/gaussian_samples/accept_reject/generate_gaussian_samples.py | Python | mit | 17,367 | [
"Gaussian"
] | 6657074458c89c0b9485c23e8f87ee055fd36fc26e134f6f86478f67e436dda4 |
# -*- coding: utf-8 -*-
'''
utilities.py
'''
import os
import tarfile
from scipy.spatial import cKDTree
import numpy as np
from shutil import rmtree, copyfile
from .pycompat import iteritems, SafeConfigParser
from netCDF4 import Dataset
from logging import getLogger
from .log import LOG_NAME
from .share import TIMESTAM... | jhamman/RVIC | rvic/core/utilities.py | Python | gpl-3.0 | 14,862 | [
"NetCDF"
] | b1a637adf6cd64517dcf495c3d57af17fe2147d66489e5ffece2f8b930a36abe |
# 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 Prokka(Package):
"""Prokka is a software tool to annotate bacterial, archaeal and viral
... | LLNL/spack | var/spack/repos/builtin/packages/prokka/package.py | Python | lgpl-2.1 | 1,155 | [
"BLAST",
"BioPerl"
] | a947e044fcefc6cd97bfda829c25cca12bb75cc6d2907aeb96ded383ec3ebef3 |
## @mainpage SWAP Device Management Tool (GUI version)
# @section intro_sec Introduction
# SWAPdmt is management tool created to configure and monitor SWAP networks. This tool is entirely based on pyswap, our Python
# SWAP library. SWAPdmt can be used in different manners:
#
# - As a network sniffer: SWAPdmt lets you m... | panStamp/python_tools | swapdmt/readme.py | Python | gpl-2.0 | 995 | [
"VisIt"
] | f35f6f5b9c3aea5626c64ea522cad87030b415283eb0d6e9e9818105fedede9f |
'''
bilat_filter.py
Experiment with OpenCV for FITS files.
http://docs.opencv.org/trunk/doc/py_tutorials/py_tutorials.html
Author: S.T. Castle
Created: 20150213
'''
import numpy as np
import cv2
import fileinput
from matplotlib import pyplot as plt
import sys
from fits-proc import FitsProc
def main():
for file... | castlest/shell-detection | convolutions/std-kernel/convolutions-plot.py | Python | bsd-3-clause | 1,711 | [
"Gaussian"
] | f0638f15e3ba446252255cc2a87bc03a1e0560160f677aed406a4fe25776faf6 |
from numpy import array
from mayavi.scripts import mayavi2
from simphony.cuds.particles import Particles, Particle, Bond
from simphony.core.data_container import DataContainer
points = array([[0, 0, 0], [1, 0, 0], [0, 1, 0], [0, 0, 1]], 'f')
bonds = array([[0, 1], [0, 3], [1, 3, 2]])
temperature = array([10., 20., 30... | simphony/simphony-mayavi | examples/particles_mayavi2.py | Python | bsd-2-clause | 1,383 | [
"Mayavi"
] | 34221bd782ab951fa9e40845928e0241aefc3f9fbeb84ad50dfbf1e084a43c53 |
# Copyright Contributors to the Pyro project.
# SPDX-License-Identifier: Apache-2.0
"""
This example illustrates the use of `NeuTraReparam` to run neural transport HMC [1]
on a toy model that draws from a banana-shaped bivariate distribution [2]. We first
train an autoguide by using `AutoNormalizingFlow` that learns a... | uber/pyro | examples/neutra.py | Python | apache-2.0 | 9,361 | [
"Gaussian"
] | 3b3f1e740cf78e41eb829ce6bdd59c32755a2f7e697e46fb5677c7a3c2fc69a4 |
"""
Test basic HTML form input interactions.
"""
from bok_choy.web_app_test import WebAppTest
from .pages import ButtonPage, TextFieldPage, SelectPage, CheckboxPage
class InputTest(WebAppTest):
"""
Test basic HTML form input interactions.
"""
def test_button(self):
button = ButtonPage(self.b... | drptbl/bok-choy | tests/test_inputs.py | Python | apache-2.0 | 1,190 | [
"VisIt"
] | 313031ec00186b84b689823955e14827a2c02b86d2d2966a4314a8ecc4273cf1 |
#!/usr/bin/env python
#
# Author: Oliver J. Backhouse <olbackhouse@gmail.com>
# George H. Booth <george.booth@kcl.ac.uk>
#
'''
An example of Spin-Component-Scaled-AGF2 calculation.
'''
from pyscf import gto, scf, agf2
mol = gto.M(atom='O 0 0 0; H 0 0 1; H 0 1 0', basis='cc-pvdz')
mf = scf.RHF(mol)
mf.conv_t... | sunqm/pyscf | examples/agf2/07-scs_agf2.py | Python | apache-2.0 | 722 | [
"PySCF"
] | f1969596e44f8d28373e654076c65a3f6f77862b780f2cde75e75fe60cb1f730 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2021 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
#... | jturney/psi4 | psi4/driver/qcdb/libmintsbasissetparser.py | Python | lgpl-3.0 | 18,352 | [
"Gaussian",
"Psi4"
] | 1c876e3002b604ad402b8f503cec8254da92bd452a7d7a5fbae665b9cb356ca0 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | krafczyk/spack | var/spack/repos/builtin/packages/ibmisc/package.py | Python | lgpl-2.1 | 3,484 | [
"NetCDF"
] | 1f973c4ef9b8d480aa6ae3c97a21c0b7b10caebafe38cf2d6180adb719c10d55 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | wangmiao1981/spark | python/pyspark/pandas/tests/test_series.py | Python | apache-2.0 | 120,857 | [
"Elk"
] | 64896df349db79189c156b4c1dd4f4673c3594bad86a9a7ea6406346dbd50e54 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | mfherbst/spack | var/spack/repos/builtin/packages/xios/package.py | Python | lgpl-2.1 | 7,761 | [
"NetCDF"
] | 90f975c41a42f047186ee5f67ab7c92812f59cf07965d8af767a58b4c105546a |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2015 Stanford University and the Authors
#
# Authors: Christoph Klein
# Contributors:
#
# MDTraj is free software: y... | kyleabeauchamp/mdtraj | mdtraj/geometry/rdf.py | Python | lgpl-2.1 | 3,510 | [
"Gromacs",
"MDTraj"
] | 380c074bcca309d9a3ce955057823cf19065e2da90d99fdb619a113b75e04713 |
#!/usr/bin/env python
"""
Check for presence of example files and download them.
Just call the function open_example()
For using the correct output directory just state get_example_file.OUTPUT_DIR
"""
import hashlib
import os.path
import sys
SHA256_DICT = {
"deconvolution.mzML.gz": (
"19399e4f87d8937c... | StSchulze/pymzML | example_scripts/get_example_file.py | Python | mit | 5,881 | [
"OpenMS"
] | 8cd358f21963db3bf71d09fdbd7d41c239525802bda704c5de57ecc58ec18494 |
#!/usr/bin/python
# Audio Tools, a module and set of tools for manipulating audio data
# Copyright (C) 2007-2016 Brian Langenberger
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either vers... | tuffy/python-audio-tools | test/test_formats.py | Python | gpl-2.0 | 255,854 | [
"Brian"
] | f30f3d0a784b8025a8d0e4a38fa93d516b3c6aed8aca59deaa07d33aec37e4d5 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2021 Satpy developers
#
# This file is part of satpy.
#
# satpy 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... | pytroll/satpy | satpy/readers/clavrx.py | Python | gpl-3.0 | 18,305 | [
"NetCDF"
] | dbef299f409bbd7219648c66cccb185c099c251173a56ba35e65cf8208e33226 |
# -*- coding: utf-8 -*-
"""
In this file, all the communication between the main program, and the database is handled.
"""
from __future__ import division
from warnings import warn
import pony.orm as pny
from pony.orm import db_session
import numpy as np
from Database.helpers import select_sql_point, nearest_neighb... | cLupus/neighborhood_classifier | src/Database/connector.py | Python | gpl-3.0 | 70,990 | [
"Gaussian"
] | 1131a6d0f0ad7b9b561b0ebf76841d0430ec2e443e6fc8efa38648251333b40a |
#! /usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import division, print_function, absolute_import
__author__ = "Laurent Perrinet INT - CNRS"
__licence__ = 'BSD licence'
DEBUG = True
DEBUG = False
"""
MotionParticlesFLE.py
Script file for MotionParticles
See http://invibe.net/LaurentPerrinet/Publications... | laurentperrinet/Khoei_2017_PLoSCB | scripts/MotionParticlesFLE.py | Python | mit | 96,890 | [
"Gaussian"
] | 5a7a0fdf2c77476d15610fbe651afbd052ee049d3b136a2897ea101538f39698 |
"""Variables common across modules"""
# pylint: disable=too-many-lines
import os
import ssl
import string
import sys
import platform
import re
GAM_AUTHOR = 'Jay Lee <jay0lee@gmail.com>'
GAM_VERSION = '6.17'
GAM_LICENSE = 'Apache License 2.0 (http://www.apache.org/licenses/LICENSE-2.0)'
GAM_URL = 'https://git.io/gam'
... | GAM-team/GAM | src/gam/var.py | Python | apache-2.0 | 57,466 | [
"VisIt"
] | b01efbbe76dec227396cab03160e3e9cb713d193b7a0ddfa9f5445389a13dc7c |
# coding: utf-8
class HttpBackend(object):
"""
Interface for HTTP backends
"""
def go(self, url, method, data, headers, auth, follow, agent, retries, debug):
"""
Visit a URL.
params:
url: URL to request
method: HTTP verb to use
data: ... | ahri/pycurlbrowser | pycurlbrowser/backend/base.py | Python | agpl-3.0 | 1,301 | [
"VisIt"
] | 017fd5fd61c728e3254c663b64feda418bd4f114c7448d677a831c1613a02be5 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkStreamLine(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.vtk... | nagyistoce/devide | modules/vtk_basic/vtkStreamLine.py | Python | bsd-3-clause | 493 | [
"VTK"
] | d9617cf46f16af5b9d8256ac87d7bb121150a0bfd0749ed7d30b4795e5fa3281 |
#
# Copyright (C) 2013,2014 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 l... | olenz/espresso | samples/python/lj_liquid.py | Python | gpl-3.0 | 6,660 | [
"ESPResSo"
] | 5e21618901b145cd6ed1a9a69aa52984e091249dcf947db2d6663679e6c004f5 |
"""
This script uses DNase data to classify open and closed regions in chromosomes.
E.g - it creates segmentation of the genome
"""
__author__ = 'eran'
import os
import datetime
import numpy as np
import pickle
import argparse
from config import BED_GRAPH_RESULTS_DIR
import data_provider.DiscreteTransformer
from mode... | eranroz/dnase | src/dnase_classify.py | Python | mit | 10,761 | [
"Gaussian"
] | 51e10b1eb871f45e9ade82d4fb14397da257878f142ad8e6e1b9ee38c0da7335 |
"""
Tests for scale components module.
"""
from __future__ import annotations
from math import exp
import pytest
from scitbx import sparse
from dials.algorithms.scaling.model.components.scale_components import (
ScaleComponentBase,
SHScaleComponent,
SingleBScaleFactor,
SingleScaleFactor,
)
from dia... | dials/dials | tests/algorithms/scaling/test_scale_components.py | Python | bsd-3-clause | 14,450 | [
"Gaussian"
] | ce66a68aadb0bf951bb0891f51b1c34592d9265112822678e0a0a8d62b776ce1 |
# -*- coding: utf-8 -*-
# vim: autoindent shiftwidth=4 expandtab textwidth=120 tabstop=4 softtabstop=4
###############################################################################
# OpenLP - Open Source Lyrics Projection #
# ------------------------------------------------------... | marmyshev/transitions | openlp/plugins/custom/lib/db.py | Python | gpl-2.0 | 3,404 | [
"Brian"
] | 58266207881e1d968c6e0eade99426320c5c28bb104fab5b03ad9b22dd7e2a5d |
#--------------------------------------------------------------------------
# Software: InVesalius - Software de Reconstrucao 3D de Imagens Medicas
# Copyright: (C) 2001 Centro de Pesquisas Renato Archer
# Homepage: http://www.softwarepublico.gov.br
# Contact: invesalius@cti.gov.br
# License: GNU ... | fabio-otsuka/invesalius3 | invesalius/data/surface.py | Python | gpl-2.0 | 35,564 | [
"VTK"
] | 169e9138cd23c0c47ac8309f158ccb3ad16d5a2d255aa84db6e1b4703ddf9bd7 |
#!/usr/bin/env python
#
# Copyright (C) 2020(H)
# Jozef Stefan Institute
# Max Planck Institute for Polymer Research
# Copyright (C) 2013-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
... | govarguz/espressopp | testsuite/system_test/system_test.py | Python | gpl-3.0 | 2,451 | [
"ESPResSo"
] | b18ce8bcc309126494d51e848fa61b932963f367cd5207bbe5111ea4a8e422ea |
from BAMF_Detect.postprocessors.common import Postprocessor, Postprocessors
import hashlib
class HashingPreprocessor(Postprocessor):
def __init__(self):
Postprocessor.__init__(
self,
name="Hashes",
author="Brian Wallace (@botnet_hunter)",
date="March 14th, 2... | bwall/bamfdetect | BAMF_Detect/postprocessors/Hashes.py | Python | mit | 811 | [
"Brian"
] | eff8323ccd41d3ca295a22e0d42e4d97e0c18084cfc47f679394db8b7b854550 |
#!/usr/bin/env python
import os,re,vcf
from optparse import OptionParser
#
# vcf_to_haplogrep
# used on mtDNA data in VCF format.
# especially the 1kg and merriman sequences data.
#
def vcf_to_haplogrep(vcf_input,hgrep_output,species,min_depth,ploidy):
vcf_reader = vcf.Reader(open(vcf_input,'r'),strict_white... | theboocock/ancient_dna_pipeline | bin/vcf_to_haplogrep.py | Python | mit | 5,011 | [
"BWA"
] | f653a00f9f1ebbbed05e2360fb9993efdbf58ad1a6a1bdce4d651df826878aa2 |
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
from DIRAC import gLogger
from DIRAC.Core.Base.Client import Client
class VMClient(Client):
def __init__(self):
"""c'tor
:param self: self reference
"""
Client.__init__(self)
self.log ... | DIRACGrid/VMDIRAC | VMDIRAC/WorkloadManagementSystem/Client/VMClient.py | Python | gpl-3.0 | 437 | [
"DIRAC"
] | 85b9e0fcf4a24dae5d3c9a90c91321090abc6ad1e657450b9a732a0270868fb5 |
'''
Created on Jun 6, 2012
@author: mkiyer
'''
import sys
import logging
import argparse
import collections
import subprocess
import pysam
import chimerascan
from chimerascan.lib import config
from chimerascan.lib.seq import DNA_reverse_complement
from chimerascan.lib.base import check_executable, LibraryTypes
from ... | tectronics/chimerascan | chimerascan/pipeline/transcriptome_to_genome.py | Python | gpl-3.0 | 13,308 | [
"Bowtie",
"pysam"
] | dffc9626e0ba2ab5cdb7602013ac1817509de07ac090993902d160ecc84a37d9 |
#!/usr/bin/python
from __future__ import print_function
import docopt
from timestream.manipulate import setup_console_logger
from timestream.manipulate.netcdf import ts_to_tsnc
CLI = """
USAGE:
timestreamToNetCDF.py -i IN_TIMESTREAM -o OUT_NETCDF
OPTIONS:
-i IN_TIMESTREAM Input timestream
-o OUT_NETCDF ... | borevitzlab/timestreamlib | scripts/tscli/timestreamToNetCDF.py | Python | gpl-3.0 | 498 | [
"NetCDF"
] | 731cadb980d37743b1e7a8a24e354c4fc34cc97bb3566429bb3c37bc1c3873ef |
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