text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
value | license stringclasses 15
values | size int32 12 1.05M | keyword listlengths 1 23 | text_hash stringlengths 64 64 |
|---|---|---|---|---|---|---|---|
"""
Collection of data and unit converters
Input
=====
- 'M' refers to a matrix/array.
- 'S' refers to a scalar.
@author: kmu
@since: 17. aug. 2010
"""
# Built-in
import os
# Additional
from numpy import uint16, int8, int16, float32, float64, isnan, load
#Own
from pysenorge.set_environment imp... | kmunve/pysenorge | pysenorge/converters.py | Python | gpl-3.0 | 3,374 | [
"NetCDF"
] | 4c2b11c35116dabe029d13dff322a45c152fe8712a2470a17916c53e1cfad133 |
import concurrent.futures
import datetime
import fractions
import json
import logging
import math
import os
from pkg_resources import DistributionNotFound, get_distribution
import psutil
import struct
from tempfile import TemporaryDirectory
import threading
import time
import numpy
import tifftools
try:
__version... | DigitalSlideArchive/large_image | utilities/converter/large_image_converter/__init__.py | Python | apache-2.0 | 34,861 | [
"NetCDF"
] | bbf163bb934aec5130bd6741b8f7d0b1fbc88df1aa6f3ee0e6293f49fb118e70 |
##
# Copyright 2009-2016 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | ocaisa/easybuild-easyblocks | easybuild/easyblocks/w/wrf.py | Python | gpl-2.0 | 16,882 | [
"NetCDF"
] | e35efc731dcd288c3bb91efc439dd5cc1f4f023df686af4ab7672a0adc15203b |
# =========================================================================
#
# Imports
#
# =========================================================================
import unittest
from .context import basis
import numpy as np
import numpy.testing as npt
from numpy.polynomial import Polynomial as P # import the Leg... | marchdf/dg1d | tests/test_basis.py | Python | apache-2.0 | 5,033 | [
"Gaussian"
] | 68af1731d64aa68fca08baf552993e46c9845c64f200ff4442cadce684122546 |
##############################################################################
# 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/r-bsgenome/package.py | Python | lgpl-2.1 | 2,532 | [
"Bioconductor"
] | f29b8ce9677aea7c62424e22a25b7a00f31b1a679636a377c8aba2a71650f85a |
"""
Numba-specific errors and warnings.
"""
import abc
import contextlib
import os
import sys
import warnings
import numba.core.config
import numpy as np
from collections import defaultdict
from numba.core.utils import chain_exception
from functools import wraps
from abc import abstractmethod
# Filled at the end
__a... | stonebig/numba | numba/core/errors.py | Python | bsd-2-clause | 22,392 | [
"VisIt"
] | 70663d24ec1d31bbfe22eb08a3719333471820d79599dee491dfb796f18c2ba8 |
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
import sys
import os
import numpy as np
import numpy.testing as npt
import scipy.sparse
import scipy.io
from mdtraj import io
from msmbuilder import tpt
from msmbuilder.scripts import FindPaths
from msmbuilder... | mpharrigan/msmbuilder | tests/test_tpt.py | Python | gpl-2.0 | 5,760 | [
"MDTraj"
] | 4bfc3532c8039123b98a06c356e447d2391fc6f5e9c991a289200773f9c9fb2b |
# Copyright 2007-2020 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 your option) any later ve... | dnjohnstone/hyperspy | hyperspy/tests/component/test_component_active_array.py | Python | gpl-3.0 | 2,393 | [
"Gaussian"
] | ac0b1a2f6e9d99b9c9f3f30d86db5c7d588cdc5a303a5ad7d84a8987133bebf8 |
"""
Copyright (c) 2015 Andreea Georgescu
Created on Thu Nov 20 22:52:11 2014
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.
... | Andreea-G/Codds_DarkMatter | src/experiment.py | Python | gpl-2.0 | 39,592 | [
"DIRAC",
"Gaussian"
] | 875abd001e51ec8bf5fa32a9bb485a8c0998e68d04103c724bc7a49bf74d5a0a |
# -*- coding: utf-8 -*-
"""
Created on Wed Oct 4 17:04:20 2017
A setup script that creates an .exe file of the project inside the "build" folder
USAGE:
From terminal or cmd, write:
python setup.py bdist_msi <- for windows installer
python setup.py bdist_mac <- for mac installer (only works if run... | danmark2312/Project-Electricity | setup.py | Python | gpl-3.0 | 1,171 | [
"MOE"
] | dc5c421d39a98bde66b97685347830f3507d998fab87338fd556f8ee54809743 |
#!/usr/bin/env python
# -*- encoding: utf-8 -*-
from __future__ import unicode_literals
import bindings as bi
import sys
PY3 = sys.version_info[0] == 3
str_type = str if PY3 else (str, unicode)
# We specify these not as real types, but as parameter annotations in the docstrings
class PythonTypeTranslatorForCheck(bi.T... | mathemage/h2o-3 | h2o-bindings/bin/gen_python.py | Python | apache-2.0 | 24,995 | [
"Gaussian"
] | e04ef9c83942e77b85102276fb53cb582fe57bd52885ace0de591ed4f10a9a54 |
import numpy as np
#formate the xyz file to vtk file format, which could be imported by paraview
#global variables
cal_dist=lambda p1,p2:np.sqrt(np.sum((p1-p2)**2))
POLY_LIB={'tectrahedra':['As','P','Cr'],'pyramid':['Pb'],'octahedron':['Sb','Fe','Cd','Cu','Zn']}
HT_CUTOFF={'As':6.0,'Pb':6.0,'Fe':0.0,'Sb':0.0,'P':0.,'... | jackey-qiu/genx_pc_qiu | supportive_functions/formate_xyz_to_vtk.py | Python | gpl-3.0 | 12,449 | [
"ParaView",
"VTK"
] | 0b61f3751b06090cd4690da889fcfb6cb8818a24d59809eb59a01adb515099ef |
# -*- coding: utf-8 -*-
"""
Created on Wed Mar 25 10:46:06 2015
@author: Paco
"""
"""Copyleft 2010 Forrest Sheng Bao http://fsbao.net
PyEEG, a Python module to extract EEG features, v 0.02_r2
Project homepage: http://pyeeg.org
**Data structure**
PyEEG only uses standard Python and numpy data structures,
so you need t... | franblas/eegChallenge | src/pyeeg.py | Python | mit | 22,783 | [
"VisIt"
] | ed66fc528f743d04a9371b4a068c405e510b6c8dfa31d51818813097541acbef |
"""
Student Views
"""
import datetime
import logging
import uuid
import json
import warnings
from collections import defaultdict
from urlparse import urljoin, urlsplit, parse_qs, urlunsplit
from django.views.generic import TemplateView
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
i... | synergeticsedx/deployment-wipro | common/djangoapps/student/views.py | Python | agpl-3.0 | 116,468 | [
"VisIt"
] | 5ef958e151f66fdeeea8348d95e56d51c933bb006a0924d4040f633fc07fb586 |
import sys
import math
from openfermion.chem import MolecularData
from openfermionpsi4 import run_psi4
# Set molecule parameters.
basis = 'sto-3g'
multiplicity = 1
bond_length_interval = 0.2
n_points = 10
# Set calculation parameters.
run_scf = 1
run_mp2 = 1
run_cisd = 0
run_ccsd = 0
run_fci = 1
delete_input = True
d... | psi4/psi4meta | conda-recipes/openfermionpsi4/tests/demo.py | Python | gpl-2.0 | 2,293 | [
"Psi4"
] | 1410df5289b873735edb970806d29f713d3f305b0c7de3d09428c1a879c7abf9 |
# MIT License
#
# Copyright (c) 2016 Daily Actie
#
# 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 limitation the rights
# to use, copy, modify, merge, ... | DailyActie/Surrogate-Model | surrogate/mutation/mutGaussian.py | Python | mit | 2,777 | [
"Gaussian"
] | d8e86da4e903495a2bac42172561fb3b8595fde4856aa43b9ea7bfa8d4a0e080 |
"""
This file is part of Giswater 3
The program is free software: you can redistribute it and/or modify it under the terms of the GNU
General Public License as published by the Free Software Foundation, either version 3 of the License,
or (at your option) any later version.
"""
# -*- coding: utf-8 -*-
from ..dialog imp... | Giswater/giswater_qgis_plugin | core/toolbars/om/visit_button.py | Python | gpl-3.0 | 706 | [
"VisIt"
] | 51ffc36bc76f89d726ecaca4e03ca015954ff1fcbd1a109cfb551f6204f1993f |
# -*- coding: utf-8 -*-
def VtkCargaIdsKPts(recordGrid):
etiqKPt= VtkCreaStrArraySetData(recordGrid.setName,"pnts","codigo")
recordGrid.uGrid.PointData.SetStrings(etiqKPt)
def VtkDibujaIdsKPts(nmbUGrid,setName,renderer):
'''Draw the points labels.'''
st= preprocessor.getSets.getSet(setName)
numKPtsDI= st.si... | lcpt/xc | python_modules/postprocess/xcVtk/CAD_model/vtk_define_kpoints_cad.py | Python | gpl-3.0 | 1,589 | [
"VTK"
] | 86ce33f697986a2116f116560fab5cbecae02cafc0a6f78e499031d3540c7e51 |
import copy
import json
from collections.abc import Mapping
from inspect import isclass
from .base import Environment, Object
from .naming import Namable, frozendict
from .typing import Type, TypeCheck, TypeFactory, TypeMetaclass
class Empty(object):
"""The Empty sentinel representing an unspecified field."""
pa... | wickman/pystachio | pystachio/composite.py | Python | mit | 11,350 | [
"Brian"
] | bf6562e59746a4a79f5101bd04b02a30ed393a6eabc03d943a50524acb6c8a70 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | modeling/modeling/galaxy.py | Python | agpl-3.0 | 46,759 | [
"Galaxy",
"Gaussian"
] | 6a9c0df59fc28546ed443922c1928ca52677dd0cf1308a3b990673e21581f690 |
#!/bin/env python3
import re
from VASP import readGjf, writeXYZ
import sys
space = re.compile(r'\s+')
if len(sys.argv) == 1:
print("")
print("Usage: %s line1,line2,.... T/F vaspfile" % sys.argv[0].split('/')[-1])
print("the format of line1,line2,... can be either x or x-x")
print("try again")
pri... | Mabinogiysk/VASP-script | gjf2xyz.py | Python | gpl-2.0 | 876 | [
"VASP"
] | e952e1c9413f8381ed62473a944ad94f90dedff835135969f97bc251e4bd3169 |
# -*- coding: utf-8 -*-
"""
A real simple app for using webapp2 with auth and session.
It just covers the basics. Creating a user, login, logout
and a decorator for protecting certain handlers.
Routes are setup in routes.py and added in main.py
"""
# standard library imports
import logging
import jso... | wilsoncampusano/gae-boilerplate | bp_includes/handlers.py | Python | lgpl-3.0 | 64,076 | [
"VisIt"
] | e45e08136cef7ec377843e6ad94d40d7b85ee0b7ebc64b57fe8a9847711ce6c9 |
# -*- coding: utf-8 -*-
"""Algorithms for spectral clustering"""
# Author: Gael Varoquaux <gael.varoquaux@normalesup.org>
# Brian Cheung
# Wei LI <kuantkid@gmail.com>
# Andrew Knyazev <Andrew.Knyazev@ucdenver.edu>
# License: BSD 3 clause
import warnings
import numpy as np
from scipy.linalg im... | sergeyf/scikit-learn | sklearn/cluster/_spectral.py | Python | bsd-3-clause | 28,258 | [
"Brian",
"Gaussian"
] | cb5ce3b6dc965d720909dbc4ebff7c251fbbdd5f2b85b5d4836b3dd83939445c |
"""Script for running a tsunami inundation scenario for Busselton, WA Australia.
Source data such as elevation and boundary data is assumed to be available in
directories specified by project.py
The output sww file is stored in directory named after the scenario, i.e
slide or fixed_wave.
The scenario is define... | AuScope/VHIRL-Portal | src/main/resources/org/auscope/portal/server/scriptbuilder/templates/run_busselton.py | Python | gpl-3.0 | 10,162 | [
"NetCDF"
] | 952842a4e7c81228537836ee6599e8f061fb801fda6e81d6811be93c2cf5c2d6 |
"""
Some extras on test_xray. Split up so Travis can parallelize them.
"""
import os
import sys
import warnings
import tables
import numpy as np
from scipy import stats
from thor import utils
from thor import math2
from thor import utils
from thor import xray
from thor import parse
from thor import structure
from t... | tjlane/thor | test/xray/test_xray2.py | Python | gpl-2.0 | 4,945 | [
"MDTraj"
] | 94a606326c9f488709106fa35a44fab02bf4aac0f42bc1b5166e2a275636864e |
from flask import Flask, render_template, request, redirect, url_for, Response, send_from_directory, jsonify, flash
from flask_login import LoginManager, current_user, login_user, logout_user, login_required
from werkzeug.utils import secure_filename
from werkzeug.urls import url_quote_plus
from urllib.parse import url... | Rosuav/appension | glitch/server.py | Python | artistic-2.0 | 14,892 | [
"VisIt"
] | 11f2b389f75d9be192a2e09c040cb99463cb1b0a0cc7bc29b8f3785a10e4565a |
"""
Chooses a set of components to make a running program.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _, logger
import locale
import collections
from zeroinstall.injector.reader import MissingLocalFeed
from zeroinstall.injector im... | dabrahams/0install | zeroinstall/injector/solver.py | Python | lgpl-2.1 | 34,098 | [
"VisIt"
] | 4c32673ec2a80025475507d6da30e458d48e0dd45171032aba71457f5ae0e4a3 |
########################################################################
# $HeadURL $
# File: FTSAgent.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/05/31 10:00:13
########################################################################
""" :mod: FTSAgent
==============
.. module: FTSAgent
:syno... | avedaee/DIRAC | DataManagementSystem/Agent/FTSAgent.py | Python | gpl-3.0 | 39,540 | [
"DIRAC"
] | b95f4775a605332be0f3d7ad13036cc66a9e90392121f4429977e33c5f6fdd89 |
"""
Functions to operate on polynomials.
"""
from __future__ import division, absolute_import, print_function
__all__ = ['poly', 'roots', 'polyint', 'polyder', 'polyadd',
'polysub', 'polymul', 'polydiv', 'polyval', 'poly1d',
'polyfit', 'RankWarning']
import re
import warnings
import numpy.core.... | jjas0nn/solvem | tensorflow/lib/python2.7/site-packages/numpy/lib/polynomial.py | Python | mit | 37,972 | [
"Gaussian"
] | 58e47b492a2a15b5b8da8fa0aff31eb00ca600f99e263fdd00b11cb0eb91a770 |
##############################################################################
# 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... | EmreAtes/spack | var/spack/repos/builtin/packages/r-affycomp/package.py | Python | lgpl-2.1 | 1,774 | [
"Bioconductor"
] | d48e40a7f98a0c7bd154bcd17888eb1ad50b99765ffd766af052a9c7dc795bac |
"""
Potential function derivative definitions.
In this code potentials are defined as closures.
This allows one to instantate a parameterized potential once and pass around the
resulting function as a closure without needing to thread the potential parameters
through the code.
"""
from math import exp, pi
#
# equatio... | HNoorazar/PyOpinionGame | opiniongame/potentials.py | Python | gpl-3.0 | 1,936 | [
"Gaussian"
] | 30e78e2689c28e8ed31fa05335a9403dc531f5b0b374e4a77f3f2e8ef0539876 |
# Copyright 2008-2013 Nokia Siemens Networks Oyj
#
# 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... | ktan2020/legacy-automation | win/Lib/site-packages/robot/model/statistics.py | Python | mit | 2,603 | [
"VisIt"
] | 8371a38985631b784723d3e5fffe4caa43dd89fa1641dcaadf45e691d1201406 |
"""
Authors: Tim Bedin (Tim.Bedin@csiro.au)
Tim Erwin (Tim.Erwin@csiro.au)
Damien Irving (irving.damien@gmail.com)
Copyright 2014 CSIRO
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 Li... | paolap/cwsl-mas | cwsl/vt_modules/vt_xmltonc.py | Python | apache-2.0 | 7,814 | [
"NetCDF"
] | c12c1af1381746d2ee4c7ae35b34df2b6461e4503fec332c390a8e8e2d8508ae |
# -*- coding: utf-8 -*-
"""
GUI for CogStat.
"""
# Splash screen
import os
import sys
import importlib
from PyQt5 import QtGui, QtWidgets
from PyQt5.QtCore import Qt
app = QtWidgets.QApplication(sys.argv)
pixmap = QtGui.QPixmap(os.path.join(os.path.dirname(os.path.abspath(__file__)), 'resources',
... | cogstat/cogstat | cogstat/cogstat_gui.py | Python | gpl-3.0 | 47,231 | [
"VisIt"
] | d87f0459aa652ac2fba15720ccecf441d13a5a16a779e224fddde14288037d19 |
###############################################################################
# ilastik: interactive learning and segmentation toolkit
#
# Copyright (C) 2011-2014, the ilastik developers
# <team@ilastik.org>
#
# This program is free software; you can redistribute it and/or
# mod... | ilastikdev/ilastik | setup_mac.py | Python | gpl-3.0 | 10,462 | [
"VTK"
] | 328bddc49e1168da47219a9fcc2141df89197cbce44e1598ba18db0ec8a9fa00 |
import numpy as np
from astropy.table import Table
from astropy.io import fits
import matplotlib.pyplot as plt
import matplotlib
import pickle
from os.path import isfile, join
from os import listdir
from astropy.time import Time
pkl_file = open('wl.pkl', 'rb')
wl = pickle.load(pkl_file)
pkl_file.close()
#Now ... | peraktong/Cannon-Experiment | Diagnostic/0321_diagnostic_plot.py | Python | mit | 13,264 | [
"VisIt"
] | f8cf143613723cee3d5f36d68528bc2f48393c6e91c5d5390144b6f6b57f1024 |
# -*- coding: utf-8 -*-
"""
[Python 2.7 (Mayavi is not yet compatible with Python 3+)]
Created on Mon Feb 09 18:11:08 2015
@author: Ryan Stauffer
https://github.com/ryanpstauffer/market-vis
market-vis v0.01
Market Visualization Prototype
Main script
"""
from datetime import datetime
from timeit import de... | ryanpstauffer/market-vis | marketvis/marketvis.py | Python | mit | 2,766 | [
"Mayavi"
] | 695c81ecd017c73b1a18cad8f77bbb2cdddbabc619b59c2a0fb26f3ef7b77231 |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
from parsimonious.grammar import Grammar
from parsimonious.nodes import NodeVisitor
class EntryParser(NodeVisitor):
def __init__(self, grammar, text):
self.entry = {}
ast = Grammar(grammar).parse(text)
self.visit(ast)
def visit... | codeyash/plugins | PyPlugins/PhpParser/py/p1.py | Python | apache-2.0 | 1,684 | [
"VisIt"
] | c2d5f4d8ecf8582360577cac69e7535e73f862b27677f073dfd81e7e12e115a4 |
#
# 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... | mgusenbauer/espresso | samples/python/debye_hueckel.py | Python | gpl-3.0 | 7,721 | [
"ESPResSo"
] | d76f0eda3929c2a6ff0d7bb24d65960d9ff732cbdbc060b07dad3f8d30d0cb7e |
"""
netcdftrajectory - I/O trajectory files in the AMBER NetCDF convention
More information on the AMBER NetCDF conventions can be found at
http://ambermd.org/netcdf/. This module supports extensions to
these conventions, such as writing of additional fields and writing to
HDF5 (NetCDF-4) files.
A Python NetCDF modul... | suttond/MODOI | ase/io/netcdftrajectory.py | Python | lgpl-3.0 | 24,293 | [
"ASE",
"Amber",
"LAMMPS",
"NetCDF",
"OVITO",
"VMD"
] | dc718955c88ca82c1e425f5e89602f718dad62839a4a8edbf02879460695ef93 |
# $HeadURL: $
""" Statistics
Module containing little helpers that extract information from the RSS databases
providing information for comparisons and plots.
"""
import datetime
# DIRAC
from DIRAC import S_ERROR, S_OK
from DIRAC.ResourceStatusSystem.Client.... | avedaee/DIRAC | ResourceStatusSystem/Utilities/Statistics.py | Python | gpl-3.0 | 8,907 | [
"DIRAC"
] | 2cf75ea733f7e400c3a71639e5a58ee5ac04cbdc511256fd07d88636c184a1a9 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
import os
from datetime import datetime
from django.test import SimpleTestCase, ignore_warnings
from django.utils import html, safestring, six
from django.utils._os import upath
from django.utils.deprecation import RemovedInDjango20Warning
from django.ut... | hackerbot/DjangoDev | tests/utils_tests/test_html.py | Python | bsd-3-clause | 10,708 | [
"ADF"
] | a566040ed5350e66e0d1a5749f68091b9c5666e356f9c48ba0be95d7f5abdec5 |
import os
import tempfile
import sys
import pymbar
import numpy as np
import pandas as pd
import simtk.openmm.app as app
import simtk.openmm as mm
import simtk.unit as u
import mdtraj as md
# 0.2 * 1000 / 18.015
temperature = 300.0 * u.kelvin
pressure = 1.0 * u.atmospheres
stderr_tolerance = 0.0001
ionicStrength = 2.... | kyleabeauchamp/DBayes | dbayes/test_ion.py | Python | gpl-2.0 | 2,206 | [
"MDTraj",
"OpenMM"
] | a5ed5b209efda615c912f8d8fdc202258f709d8025588cc80af695475258e568 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 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
#... | CDSherrill/psi4 | psi4/driver/qcdb/vib.py | Python | lgpl-3.0 | 50,016 | [
"Avogadro",
"Psi4"
] | 69125035ddbcc921cc3fe50d08dde7ac2ed0b16b420ead3bde8409e23943d019 |
'''
Created on Feb 2, 2010
@author: Brian Thorne
'''
from scipysim.actors.logic import Compare
class LessThan(Compare):
def compare(self, event):
return event.value < self.threshold
| mm318/scipysim-nogui | scipysim/actors/logic/lessthan.py | Python | gpl-3.0 | 196 | [
"Brian"
] | 111e1b8b96e3fe7a637217dc4dbd33cbda4b06f3c2b7b020d9bd400f9b01e45f |
"""
pymel ipython configuration
Current Features
----------------
tab completion of depend nodes, dag nodes, and attributes
automatic import of pymel
Future Features
---------------
- tab completion of PyNode attributes
- color coding of tab complete options
- to differentiate between methods and attributes
... | david-lassonde-adsk/pymel | pymel/tools/ipymel.py | Python | bsd-3-clause | 29,006 | [
"VisIt"
] | b6fede273784967bad81d7a6c1541837dd41ce70aefba7532e991f3132025d01 |
import re
from PyQt5 import QtWidgets, QtCore
import peacock
import mooseutils
from plugins.ExodusPlugin import ExodusPlugin
class ExodusPluginManager(QtWidgets.QWidget, peacock.base.PluginManager):
def __init__(self, plugins=[]):
super(ExodusPluginManager, self).__init__(plugins=plugins, plugin_base=Exod... | liuwenf/moose | python/peacock/ExodusViewer/ExodusPluginManager.py | Python | lgpl-2.1 | 4,887 | [
"VTK"
] | e9e3849fb40a54b01632537f52a0914b59b49298c99ed8c3d92453da0403948e |
# -*- coding: utf-8 -*-
#
# Copyright (c) 2016, 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.
"""Test coupled cluster logfiles"""
import os
import unittest
import numpy
__filedir__ = os.path.realpath(os.path.dirn... | Schamnad/cclib | test/data/testCC.py | Python | bsd-3-clause | 815 | [
"cclib"
] | 384d07072ede49b8d23c2dea34227680afdd877a6fea70014588499c7e9565bb |
__author__ = 'nikita_kartashov'
# -*- coding: utf-8 -*-
import re
from pattern.web import plaintext
from pattern.web import Crawler, BREADTH, FILO
import inspect
class CustomCrawler(Crawler):
def __init__(self, url, depth, index):
Crawler.__init__(self, links=[url])
re_text = u"""[абвгдеёжзийклмн... | nkartashov/NKrawler | crawler.py | Python | gpl-2.0 | 1,992 | [
"VisIt"
] | 7a949e80dbe11f3ee61022788613a05fe5906a3eb6d60db9ebe7e6e4d3225ee9 |
import openvoronoi as ovd
import ovdvtk
import time
import vtk
import truetypetracer as ttt
import math
def drawLine(myscreen, pt1, pt2, lineColor):
myscreen.addActor(ovdvtk.Line(p1=(pt1.x, pt1.y, 0), p2=(pt2.x, pt2.y, 0), color=lineColor))
def drawArc(myscreen, pt1, pt2, r, cen, cw, arcColor):
# draw arc a... | aewallin/openvoronoi | python_examples/faceoffset_1.py | Python | lgpl-2.1 | 6,980 | [
"VTK"
] | 5e63b580189b1f1821ddec7be44edbed20f8f234477ab30f87af9eca89126b36 |
from __future__ import print_function
import sys, os
from ShapeAnalysisModule import ShapeAnalysisModuleWrapper
try:
from configparser import SafeConfigParser
except ImportError:
from ConfigParser import SafeConfigParser # python 2.x
if len(sys.argv) != 2:
print("\n\nUsage: ./SlicerSALT --no-main-window --pyth... | NIRALUser/SPHARM-PDM | CommandLineTool/SPHARM-PDM.py | Python | apache-2.0 | 8,056 | [
"VTK"
] | 4eb816c7eb8ec4aee011c882feebfee602b143ef06dbbc61fba91748cb33e64a |
# Copyright 2017,2018,2019,2020,2021 Sony Corporation.
# Copyright 2021 Sony Group 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-... | sony/nnabla | python/test/test_variable.py | Python | apache-2.0 | 11,689 | [
"VisIt"
] | ee62034dd951da016333d8586df5883ccb079ec34609bcef280a50f4550da0a8 |
#-------------------------------------------------------------------------------
# . File : CHELPGCharges.py
# . Program : MolarisTools
# . Copyright : USC, Mikolaj Feliks (2015-2018)
# . License : GNU GPL v3.0 (http://www.gnu.org/licenses/gpl-3.0.en.html)
#-----------------------------------------------... | mfx9/molaris-tools | MolarisTools/Other/CHELPGCharges.py | Python | gpl-3.0 | 9,388 | [
"Gaussian",
"ORCA"
] | 893596837e3f94a70b14ae22791ccb8248ab66e77e64e50e1cc7ae9f64977cd0 |
import logging, threading, sys, os, time, subprocess, string, tempfile, re, traceback, shutil
from galaxy import util, model
from galaxy.model import mapping
from galaxy.model.orm import lazyload
from galaxy.datatypes.tabular import *
from galaxy.datatypes.interval import *
from galaxy.datatypes import metadata
impor... | dbcls/dbcls-galaxy | lib/galaxy/jobs/__init__.py | Python | mit | 34,209 | [
"Galaxy"
] | c11cad6d0752ba93b5dd97b90ed7910aed75593c214e9968d33dfdd73e8c05ac |
#!/usr/bin/env python3
# vim: set encoding=utf-8 tabstop=4 softtabstop=4 shiftwidth=4 expandtab
#########################################################################
# Copyright 2012-2013 Marcus Popp marcus@popp.mx
# Copyright 2016- Martin Sinn m.sinn@gmx.de
##... | smaiLee/smarthome | plugins/visu_websocket/__init__.py | Python | gpl-3.0 | 21,998 | [
"VisIt"
] | 8df296db22af09092d420fcd0c708ee03491cc4432674b4d7a3e56b60f4d9983 |
#!/usr/bin/env python
## category General
## desc Calculate the inner mate-pair distance from two BAM files
'''
Calculate the inner mate-pair distance from two BAM files
With paired-end reads, knowing the inner mate-pair distance is key for some
downstream analyses or mapping. This value can be estimated using wet-lab... | ngsutils/ngsutils | ngsutils/bam/innerdist.py | Python | bsd-3-clause | 4,800 | [
"pysam"
] | bd246170cab7ee2a02b8aeb2dccc9f9fd6a10eb44042769114e7a94201c9abdd |
#!/usr/bin/env python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://setuptools.readthedocs.io/en/latest/easy_install.html
""... | astaninger/speakout | venv/lib/python3.6/site-packages/setuptools/command/easy_install.py | Python | mit | 87,050 | [
"VisIt"
] | 80a7446a6bd82e59f80601ee9128f3684a026dd120e865ce9a5b4f7ad7a24a62 |
# Copyright 2002 by Katharine Lindner. 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.
"""handles true random numbers supplied from the the web server of fourmilab. Based on atm... | bryback/quickseq | genescript/Bio/HotRand.py | Python | mit | 2,065 | [
"Biopython"
] | 51b04cd47d90620150557ba4f24c81d7c2e865acf6fd82900c36f098eca16c0b |
#!/usr/bin/env python
"""
Connects to the URL specified and outputs builds available at that
DSN in tabular format. USCS Test gateway is used as default.
build description
"""
import sys
import urllib
if sys.version_info[:2] >= ( 2, 5 ):
import xml.etree.ElementTree as ElementTree
else:
from galaxy import ... | volpino/Yeps-EURAC | cron/parse_builds.py | Python | mit | 1,621 | [
"Galaxy"
] | 19146f8e7588ed2f1386c9c3f67770b7b8107dec3655a4025f87edab58a37540 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
def test_sparse_ci2():
import math
import psi4
import forte
import itertools
import numpy as np
import pytest
from forte import forte_options
ref_fci = -5.623851783330647
psi4.core.clean()
# need to clean the options otherwise thi... | evangelistalab/forte | tests/pytest/sparse_ci/test_sparse_ci2.py | Python | lgpl-3.0 | 3,031 | [
"Psi4"
] | 518706648ecdfa78f37996cd55250e2967b8e2addc01c34fce67c169fb7077ed |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
# vim:ai:sw=4:ts=8:et:fileencoding=utf-8
#
# Based on RPi Wobbulator v2.7.1
#
# Copyright (C) 2013-2014 Tom Herbison MI0IOU
# Email tom@asliceofraspberrypi.co.uk
# Web <http://www.asliceofraspberrypi.co.uk>
# Special thanks to Tony Abbey for his efforts developing v2 of the s... | mi0iou/RPi_Wobbulator | rpi_wobbulator.py | Python | gpl-3.0 | 87,332 | [
"CRYSTAL",
"VisIt"
] | deb02cd92eb0ec102e049007bead0453a1bf189f43ce6373e8d32639649f612d |
import numpy as np
from scipy.signal import gaussian
from traits.api import Callable, Enum, Instance, on_trait_change
from .base_color_function_component import BaseColorComponent, ColorNode
from .function_component import register_function_component_class
from .function_node import register_function_node_class
from ... | dmsurti/ensemble | ensemble/ctf/gaussian_function_component.py | Python | bsd-3-clause | 8,378 | [
"Gaussian"
] | c094ca7512b0107b23ea958e072b129ec59f425a8c0009cb75f1374a326ef4e3 |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/view/controls/decorated_line_edit.py | Python | gpl-2.0 | 5,915 | [
"VisIt"
] | 2f77e8c1b85f5aaf68930edbb2fddca05842253f25dd9de66e0574255160a999 |
# -*- coding: utf-8 -*-
###############################################################################
#
# PyLint tests that will never be applied for this file.
#
# Unused variables, these functions are organized so that they can be called
# from a string at runtime, from it's name being stor... | Asiant/trump | trump/extensions/symbol_aggs.py | Python | bsd-3-clause | 8,205 | [
"ADF"
] | 57633532427f846d74b061cdb15fb149fda8d17b5cf8da8544fe1a9bbb066d71 |
#/*
# *
# * OpenStreetMap for Kodi
# *
# * Copyright (C) 2015 Brian Hornsby
# *
# * 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... | brianhornsby/script.openstreetmap | resources/lib/openstreetmap.py | Python | gpl-3.0 | 10,808 | [
"Brian"
] | a4299d1119ced367b21c47b9ca2d9c40db77e2c2ad6d80421d66bc96279fc2de |
#!/usr/bin/env python
"""
--------------------------------------------------------------------------------
Created: Jackson Lee 9/29/14
This script reads in a tab delimited combined coverage file from
consolidate_coverage.py of phylogeny, protein classifications, and annotations
uses the biopython KGML libraries to ... | leejz/meta-omics-scripts | generate_kgml_graphics.py | Python | mit | 13,581 | [
"Biopython"
] | eb02dcc9bf83023755ff09184e46a2350f2536a1e924f4c8226987fd6b2182e7 |
# Adapted from Bio.AlignIO.FastaIO copyright 2008-2011 by Peter Cock.
# 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 sup... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/SearchIO/FastaIO.py | Python | gpl-2.0 | 25,543 | [
"BLAST",
"Biopython"
] | d39a0e99bfde8d6174758eb3c01d6f9ee94aa67fc1442214868882801acbad40 |
#!/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 cr... | blankclemens/tools-iuc | tools/ngsutils/filter.py | Python | mit | 28,210 | [
"pysam"
] | dc38094843119739c29b33f8bd81ac346797cbd3142773cd8f759e4e6f33ba55 |
"""Framework for getting filetype-specific metadata.
This is the same as fileinfo.py with one difference:
instead of inheriting from UserDict, we inherit directly from dict.
This capability was introduced in Python 2.2, and makes UserDict
unnecessary (along with its cousins, UserList and UserString).
This program is ... | tapomayukh/projects_in_python | sandbox_tapo/src/refs/diveintopython-pdf-5.4/diveintopython-5.4/py/fileinfo_fromdict.py | Python | mit | 2,776 | [
"VisIt"
] | dfb335ae34126db1ad299010573a4603a262e0e0ebfa66239af0448c7f9173c4 |
# coding: utf-8
from __future__ import unicode_literals
import binascii
import collections
import email
import getpass
import io
import optparse
import os
import re
import shlex
import shutil
import socket
import struct
import subprocess
import sys
import itertools
import xml.etree.ElementTree
try:
import urllib... | bosstb/HaberPush | youtube_dl/compat.py | Python | mit | 89,648 | [
"Bowtie"
] | 5af0d452eb53189193e1482741bdfcb93fe419be6b9def4bf6f6bdc494f7144e |
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of t... | BackupTheBerlios/espressopp | src/tools/analyse.py | Python | gpl-3.0 | 2,798 | [
"ESPResSo"
] | e65d111a5ac50c662d6c8a0bb60ad3c163e91cc522a7d4c5f8c2ac71a0bbb6de |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/view/register.py | Python | gpl-2.0 | 3,568 | [
"VisIt"
] | 461582458ebd987c5e04c73a34c76df467ed1def7b6df0aed53e6d1afc7c95c2 |
#!/usr/bin/env python3
"""
This script downloads the latest KeyForge card data from keyforgegame.com and processes
it to turn the highly-structured data there into a flat list of card names to descriptions
formatted to send down the chat.
"""
import common
common.FRAMEWORK_ONLY = True
import sys
import json
import re
... | andreasots/lrrbot | build_carddb_keyforge.py | Python | apache-2.0 | 7,298 | [
"Amber"
] | 5dbd204d58a86be2c0934a54e34843cfc1be16fe0586ea7f0b7757a1d22aaf96 |
import logging
import yaml
import sys
import os
import socket
def configure_logging():
logging.root.handlers = []
level = getattr(logging, os.environ.get('TROUGH_LOG_LEVEL', 'INFO'))
logging.basicConfig(stream=sys.stdout, level=level, format=(
'%(asctime)s %(levelname)s %(name)s.%(funcName)s'
... | jkafader/trough | trough/settings.py | Python | bsd-2-clause | 4,142 | [
"GULP"
] | 5ea9af2cd6f295f16fe7c8c985b1b181273c1b0a30e751c96d6c42d6d79df9d5 |
"""Base class for mixture models."""
# Author: Wei Xue <xuewei4d@gmail.com>
# Modified by Thierry Guillemot <thierry.guillemot.work@gmail.com>
# License: BSD 3 clause
from __future__ import print_function
import warnings
from abc import ABCMeta, abstractmethod
from time import time
import numpy as np
from .. impor... | sonnyhu/scikit-learn | sklearn/mixture/base.py | Python | bsd-3-clause | 14,481 | [
"Gaussian"
] | 344091cddfaf63e6abd9b6b4b026f9e9a105a52bebcc9bfb0a2c060d7bac5138 |
# -----------------------------------------------------------------------
# Copyright (c) 2009-2018 Jendrik Seipp
#
# RedNotebook is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the Licens... | jendrikseipp/rednotebook | rednotebook/help.py | Python | gpl-2.0 | 21,191 | [
"VisIt"
] | 17967f8f23118f79a8268042c96ea3b7630db2afbb5e4dceaca28e9772539b89 |
##
# gPrime - A web-based genealogy program
#
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2010 Peter Landgren
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Adam Stein <adam@csh.rit.edu>
# Copyright (C) 2011 Tim G L Lyons
# Copyright (C) 2013,2015 Paul Franklin
#
# This... | sam-m888/gprime | gprime/plug/report/endnotes.py | Python | gpl-2.0 | 8,839 | [
"Brian"
] | 166a09e3f3458eaa477f65e2bd7f9be4b721b2558c7dfcc1276e272de5c60af9 |
#!/usr/bin/env python
# Copyright (C) 2015 James Tatum
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# Thi... | jtatum/convention-stuff | scrape_registration_db.py | Python | agpl-3.0 | 5,273 | [
"ESPResSo"
] | 3798de32cf7e447e64597b76fe64d0b9245385623944ed446cedb7e39aa709c8 |
from django.test import TestCase
from openrosa.xform_reader import XFormReader
# Tutorial xform with basic data/survey types
XFORM_FILE = '../_data/test_docs/tutorial.xml'
# Basic i18n xform with translated labels
I18N_XFORM = '../_data/test_docs/zambia/Child Visit.xml'
# Translated constrai... | DHLabs/keep | keep_backend/tests/test_openrosa/test_xform_reader.py | Python | mit | 1,274 | [
"VisIt"
] | 796ce907dcc6ad94b01cde69e9001e7939b2eec37f4bafb12976b0465028a9c2 |
#Author:Chaitanya CH
#FileName: updatepaintGL.py
#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, or
# (at your option) any later version.
#
# This program is distributed in th... | BhallaLab/moose-thalamocortical | gui/updatepaintGL.py | Python | lgpl-2.1 | 11,216 | [
"MOOSE"
] | 86ab8c8366be319b2a75edb171ff517949b7ff084995514455ef7849f70cbd43 |
from __future__ import division
import numpy as np
def monkhorst_pack(size):
"""Construct a uniform sampling of k-space of given size."""
if np.less_equal(size, 0).any():
raise ValueError('Illegal size: %s' % list(size))
kpts = np.indices(size).transpose((1, 2, 3, 0)).reshape((-1, 3))
return (... | slabanja/ase | ase/dft/kpoints.py | Python | gpl-2.0 | 10,573 | [
"CRYSTAL"
] | 628961ae76852471a9741bd45a314d56a21891565557edd245c2a63d0926464e |
##############################################################################
# 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... | TheTimmy/spack | lib/spack/spack/spec.py | Python | lgpl-2.1 | 134,500 | [
"VisIt"
] | 5e64a26970e6471c9eaabd27a5ed62ee3810649a6e76a5a671397949912019a4 |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'ui/src/about.ui'
#
# Created: Wed Nov 17 12:05:52 2010
# by: PyQt4 UI code generator 4.7.3
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
class Ui_AboutDialog(object):
def setupUi(self, Ab... | ypid/series60-remote | pc/ui/ui_about.py | Python | gpl-2.0 | 8,671 | [
"VisIt"
] | c8f64ef1126b6fd254c3c16d9560c820bb314ec8187778c07b356fd4ce355912 |
#!/usr/bin/env python
# Vertex-wise mediation with TFCE
# Copyright (C) 2016 Tristram Lett
# 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
#... | trislett/TFCE_mediation | tfce_mediation/tmanalysis/STEP_1_vertex_tfce_mediation.py | Python | gpl-3.0 | 11,411 | [
"Gaussian"
] | ecccab5d9d0ba218c117ba6557ef8c3733a34f34e9770da6d09c99d5b406bbd2 |
'''
Discrete-time integrator.
Three different discrete-time integration algorithms are available:
* Backward Euler (aka Backward Rectangular)
* Forward Euler (aka Forward Rectangular)
* Trapezoidal
Note that all three implementations current assume uniform unit intervals between
input time tags.
@author: Brian ... | hardbyte/scipy-sim | scipysim/actors/math/dt_integrator.py | Python | gpl-3.0 | 5,089 | [
"Brian"
] | 190051a85d344651adc644b2d88931f1c6589d411c53a4e1f511ff4c992d3ba5 |
import collections
import operator
from functools import partial
from ..ssa import objtypes
from .. import graph_util
from ..namegen import NameGen
from ..verifier.descriptors import parseMethodDescriptor
from . import ast, ast2, boolize
from . import graphproxy, structuring, astgen, mergevariables
class DeclInfo(ob... | alexkasko/krakatau-java | krakatau-lib/src/main/resources/Lib/Krakatau/java/javamethod.py | Python | gpl-3.0 | 37,957 | [
"VisIt"
] | 40ab2fe4bd7cda2996fe9e15348700c8247cdb55643708340e9f1ec4a4ac9dbc |
""" core implementation of testing process: init, session, runtest loop. """
import enum
import fnmatch
import functools
import importlib
import os
import sys
import warnings
import attr
import py
import _pytest._code
from _pytest import nodes
from _pytest.config import directory_arg
from _pytest.config import hookim... | ekwoodrich/python-dvrip | env/lib/python3.5/site-packages/_pytest/main.py | Python | mit | 24,853 | [
"VisIt"
] | 1294ef257050854e09bb72564c72af3e6c895931bde42e8fbee7325929162e26 |
# Copyright 2019 Arie Bregman
#
# Licensed under the Apache License, Version 2.0 (the "License"); you may
# not use this file except in compliance with the License. You may obtain
# a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agree... | bregman-arie/rhoci | rhoci/jobs/routes.py | Python | apache-2.0 | 6,565 | [
"Elk"
] | d791755975e77aa38c479ea6fb54e433b8b6eac1fed8fcecfab2d5950b6aefa2 |
# -*- coding: utf-8 -*-
# Copyright 2022 Google LLC
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or... | googleapis/python-aiplatform | tests/unit/gapic/aiplatform_v1/test_metadata_service.py | Python | apache-2.0 | 361,748 | [
"Octopus"
] | 8b87494ecc910f260ff0d0f3d2c9f6db003a764a13342999b57539f4fcf3357f |
#!/usr/bin/env pypy
# -*- coding: utf-8 -*-
import argparse
import subprocess
import os
import math
import gzip
import tempfile
import urllib
import json
import ssl
__author__ = 'thomasvangurp'
__description__ = "map reads orders of magnitudes faster using STAR"
def parse_args():
"""Pass command line arguments""... | thomasvangurp/epiGBS | mapping_varcall/map_STAR.py | Python | mit | 27,043 | [
"pysam"
] | 5713ac4ae5d0bac7a987d2436658ef068c5ea31939ee54c4d7abc0e5f41646e8 |
#
# Copyright (C) 2008, Brian Tanner
#
#http://rl-glue-ext.googlecode.com/
#
# Licensed under the Apache License, Version 2.0 (the "License")
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless requi... | evenmarbles/rlglued | tests/test_message_experiment.py | Python | bsd-3-clause | 2,456 | [
"Brian"
] | 9a55a78f74ca3555f50d970e6f7e61a0057c104c42871c1908d3ca32696b5678 |
""" JobManagerHandler is the implementation of the JobManager service
in the DISET framework
The following methods are available in the Service interface
submitJob()
rescheduleJob()
deleteJob()
killJob()
"""
from __future__ import absolute_import
from __future__ import division
from __future_... | yujikato/DIRAC | src/DIRAC/WorkloadManagementSystem/Service/JobManagerHandler.py | Python | gpl-3.0 | 23,908 | [
"DIRAC"
] | d80b1031c668f1ee1e51209c0ce5faf00aa3d7af8942630389a0c9d3dd845e87 |
#!/usr/bin/env python
########################################################################
# File : dirac-admin-sort-cs-sites
# Author : Matvey Sapunov
########################################################################
"""
Sort site names at CS in "/Resources" section. Sort can be alphabetic or by country... | DIRACGrid/DIRAC | src/DIRAC/ConfigurationSystem/scripts/dirac_admin_sort_cs_sites.py | Python | gpl-3.0 | 4,219 | [
"DIRAC"
] | d3c8474b5022a4bf3d442dfcf092cc4ad6beee386a16eca2834f5e33a1a0558e |
#!/usr/bin/env python
#encoding=utf8
'''
Module describing multilayer neural network's functionality.
@author Miroslav Hlavacek <mira.hlavackuj@gmail.com>
'''
from __future__ import division
import numpy as np
import cPickle as pickle
import layer
import sectors
# TODO ... maybe try different initialization of weigh... | MiraHead/mlmvn | src/network/network_old.py | Python | gpl-2.0 | 14,638 | [
"NEURON"
] | f1611cf3dcdc755ee0d3f58dca85d1c5f2b017034f7e4b83d0ab20bdb21cdd8c |
'''
some pre-processing functions from github.com/HIPS/neural-fingerprint
'''
import numpy as np
from rdkit.Chem import MolFromSmiles
import numpy as np
from rdkit import Chem
def one_of_k_encoding(x, allowable_set):
if x not in allowable_set:
raise Exception("input {0} not in allowable set{1}:".format... | GUR9000/KerasNeuralFingerprint | mol_graph.py | Python | mit | 6,057 | [
"RDKit"
] | 9168e8005a67905c22ef2fcee7f6a1c18f4b079fe8db02fd65e8e51d8920e17d |
#!/usr/bin/env python
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# create pipeline
#
reader = vtk.vtkDataSetReader()
reader.SetFileName(VTK_DATA_ROOT + "/Data/RectGrid2.vtk")
reader.Update()
warper = vtk.vtkWarpVector()
warper.SetInpu... | hlzz/dotfiles | graphics/VTK-7.0.0/Filters/General/Testing/Python/WarpVectorImage.py | Python | bsd-3-clause | 1,372 | [
"VTK"
] | 40e5566278bc9fbe570f2dbc1b8e45f50df903b56746c50ae5d122c4145bfc44 |
import math
import random
class Ant():
"""
Ant class which navigates a graph using a pheromone based choice mechanism.
Requires an Identifier, start position in graph and an ant colony containing the graph.
Provided by antgraph and antcolony
"""
def __init__(self, ID, start_node, colony):
... | hpcarcher/2015-04-16-imperial-students | testing/ant.py | Python | gpl-2.0 | 4,889 | [
"VisIt"
] | b1c882d32b6ba3978304a96c782cf41635ed385a28e9d78e2daf310965a76fd7 |
"""
Provides rolling statistical moments and related descriptive
statistics implemented in Cython
"""
from __future__ import division
import warnings
import numpy as np
from pandas.types.common import is_scalar
from pandas.core.api import DataFrame, Series
from pandas.util.decorators import Substitution, Appender
__a... | andyraib/data-storage | python_scripts/env/lib/python3.6/site-packages/pandas/stats/moments.py | Python | apache-2.0 | 31,610 | [
"Gaussian"
] | 77439b326c74e62a3344a175f9c1bac65b76b4c1d2e8a8fece362f98fe575cf3 |
from scipy.odr import odrpack as odr
from scipy.odr import models
import numpy as np
def gaussian(B, x):
''' Returns the gaussian function for B=m,stdev,max,offset '''
return B[3] + B[2] / (B[1] * np.sqrt(2 * np.pi)) * \
np.exp(- ((x - B[0]) ** 2 / (2 * B[1] ** 2)))
def double_gaussian(B, x):
""... | ITA-Solar/helita | helita/utils/fitting.py | Python | bsd-3-clause | 13,586 | [
"Gaussian"
] | b875184f38486784394604018bc8efb15215d6be7b51895046e8706d2dc999d3 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright: (c) 2018, F5 Networks Inc.
# GNU General Public License v3.0 (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
... | alxgu/ansible | lib/ansible/modules/network/f5/bigip_asm_policy_server_technology.py | Python | gpl-3.0 | 13,639 | [
"ASE",
"Galaxy"
] | 39485af239ca221d9f9cee24ab080c589475b6361c10d822fb4577e01b026a7f |
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