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# Copyright (c) 2016-2021, The Bifrost Authors. All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditio... | ledatelescope/bifrost | python/bifrost/blocks/binary_io.py | Python | bsd-3-clause | 5,322 | [
"GULP"
] | 705e6a96a2b772f8d3a48ed3f345d597d33527929f0ba6e3de432e9b0ac6184d |
# -*- coding: utf-8 -*-
""" GIS Module
@requires: U{B{I{gluon}} <http://web2py.com>}
@requires: U{B{I{shapely}} <http://trac.gispython.org/lab/wiki/Shapely>}
@copyright: (c) 2010-2015 Sahana Software Foundation
@license: MIT
Permission is hereby granted, free of charge, to any person
obtaini... | flavour/Turkey | modules/s3/s3gis.py | Python | mit | 392,898 | [
"Amber"
] | 904f1608143a42e0a104e990548f9cac12a5e8e5d2f96c2846cb598e89c8d67d |
# -*- coding: UTF-8 -*-
# Created by mcxiaoke on 15/7/4 16:54.
__author__ = 'mcxiaoke'
'''
tzinfo使用，时区处理示例，来自Python文档
'''
from datetime import tzinfo, timedelta, datetime
ZERO = timedelta(0)
HOUR = timedelta(hours=1)
# A UTC class.
class UTC(tzinfo):
"""UTC"""
def utcoffset(self, dt):
return ZERO
... | mcxiaoke/python-labs | archives/modules/date_time_tz.py | Python | apache-2.0 | 5,204 | [
"VisIt"
] | a5dab281f232a661a887f0cb6beb4125f05844b0dd01566b3c71004bcf36e79c |
# Copyright Yair Benita Y.Benita@pharm.uu.nl
# Biopython (http://biopython.org) license applies
# sharp Ecoli index for codon adaption index.
# from Sharp & Li, Nucleic Acids Res. 1987
SharpEcoliIndex = {
'GCA':0.586, 'GCC':0.122, 'GCG':0.424, 'GCT':1, 'AGA':0.004, 'AGG':0.002, 'CGA':0.004,
'CGC':0.356, 'CGG':0.004, '... | dbmi-pitt/DIKB-Micropublication | scripts/mp-scripts/Bio/SeqUtils/CodonUsageIndices.py | Python | apache-2.0 | 910 | [
"Biopython"
] | 5453fa76b82bd679d8879de413d88b71ded3ed7c7af167c6b5207a79bddcad86 |
"""
Estimates the CPU time required for a phosim simulation of a 30-s visit. The
inputs are filter, moonalt, and moonphase, or obsHistID (an Opsim ID from
a specified (hard coded) Opsim sqlite database.
The random forest is generated (and saved as a pickle file) by
run1_cpu_generate_rf.py, using only the filter, moon... | DarkEnergyScienceCollaboration/Twinkles | python/desc/twinkles/phosim_cpu_pred.py | Python | mit | 4,141 | [
"VisIt"
] | b98dc3e1cc0bffdd17434762ed71931ac92bc26c765c09af78e48af78d63c76e |
# ===================================
# COMPARE Tapas, Telfit, Molecfit
# plotting the transmission spectra
#
# Solene 14.06.2016
# ===================================
#
import numpy as np
from astropy.io import fits
import matplotlib.pyplot as plt
from PyAstronomy import pyasl
from scipy.interpolate import interp1d
fr... | soleneulmer/atmos | compareModels.py | Python | mit | 5,232 | [
"Gaussian"
] | 09526f4d92e27e53ec5593a4f769d643256b0cc0c54c9652dc737d542ee7e66d |
#! /usr/bin/env python
"""
Get Pilots Logging for specific Pilot UUID or Job ID.
"""
from __future__ import print_function
__RCSID__ = "$Id$"
import DIRAC
from DIRAC import S_OK
from DIRAC.Core.Base import Script
from DIRAC.WorkloadManagementSystem.Client.PilotsLoggingClient import PilotsLoggingClient
from DIRAC.Wor... | petricm/DIRAC | WorkloadManagementSystem/scripts/dirac-admin-pilot-logging-info.py | Python | gpl-3.0 | 2,238 | [
"DIRAC"
] | f32701f7eec6b52a4f278feb5e419f9d4e1c384df2fd7946fe600484230ea69a |
# 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.
#
"""Find and deal with motifs in biological sequence data.
Representing DNA (or RNA or proteins) in a neural network can be difficult
since input seq... | zjuchenyuan/BioWeb | Lib/Bio/NeuralNetwork/Gene/Motif.py | Python | mit | 8,336 | [
"Biopython"
] | 3afe3e5bf265651d72f45c7ae13290b07958d9566f94f255e12ae6cc55e32f94 |
# -*- coding: utf8 -*-
from __future__ import division, with_statement
import sys
import warnings
import numpy as np
import pyfits as fits
from ..extern.six import u, b, iterkeys, itervalues, iteritems, StringIO, PY3
from ..extern.six.moves import zip, range
from ..card import _pad
from ..util import encode_ascii... | embray/PyFITS | lib/pyfits/tests/test_header.py | Python | bsd-3-clause | 98,445 | [
"BLAST"
] | 0026bb6d2ee7639efae43c6781270bb607b970571ac8d12d4d84239d7c35416b |
#
# cpair
#
# // overview
# Enumeration for colourpairs in the platform. By having a centralised
# enumeration, we can try to make the user experiences fairly consistent
# across different types of console (pygame, ncurses, etc).
#
# // license
# Copyright 2016, Free Software Foundation.
#
# This file is part of Solent... | solent-eng/solent | solent/cpair.py | Python | lgpl-3.0 | 3,576 | [
"Amber"
] | 0ea0b13cbbdc1954b59bd34ed11a31f61318a16c79b5b698724067f4fcf41022 |
# mako/pyparser.py
# Copyright 2006-2021 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""Handles parsing of Python code.
Parsing to AST is done via _ast on Python > 2.5, otherwise the co... | sqlalchemy/mako | mako/pyparser.py | Python | mit | 7,032 | [
"VisIt"
] | eb264bf2fdca92a6a230e17eda40275091c41c92f7265807fd27346f0e385dee |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright: 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
DOCUMENTATION = '''
---
module: dpkg_selections
short_description... | srvg/ansible | lib/ansible/modules/dpkg_selections.py | Python | gpl-3.0 | 2,298 | [
"Brian"
] | 3792dc7de93aef52e2fc37b6f77844ff3736051f710163b59c36618b9b6bf1a5 |
# Copyright (C) 2010-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later v... | KaiSzuttor/espresso | samples/h5md.py | Python | gpl-3.0 | 1,897 | [
"ESPResSo"
] | cce4e302f5e12122e4f4e8a558a43a4e87b2c817f0ebc0224ae399ec4851afaf |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2016 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of ... | kannon92/psi4 | psi4/driver/procedures/__init__.py | Python | gpl-2.0 | 1,150 | [
"Psi4"
] | 975005324002faee0dedcbf83d1004d40aa2db841d794fa7a4ff9e2912225abc |
''' CSHelpers
Module containing functions interacting with the CS and useful for the RSS
modules.
'''
from DIRAC import gConfig, gLogger, S_OK, S_ERROR
from DIRAC.Core.Utilities.SitesDIRACGOCDBmapping import getGOCSiteName
from DIRAC.ResourceStatusSystem.Utilities impo... | Andrew-McNab-UK/DIRAC | ResourceStatusSystem/Utilities/CSHelpers.py | Python | gpl-3.0 | 11,484 | [
"DIRAC"
] | c87552ab129982b36398c319a0018708edd478b170170f5664289c0f674a0990 |
import os
import subprocess
import unittest
import netCDF4
import numpy as np
import requests
import bald
from bald.tests import BaldTestCase
OGCFiles = ('https://raw.githubusercontent.com/opengeospatial/netcdf-ld/'
'master/standard/abstract_tests/')
class Test(BaldTestCase):
def setUp(self):
... | binary-array-ld/bald | lib/bald/tests/integration/test_ogc_conformance.py | Python | bsd-3-clause | 6,313 | [
"NetCDF"
] | 4bd3ea3aa6b9bb98abfd701a579d8aac862e514289f4fce854378c0b35aa9d33 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | fvilca/cnn_tensorflow_cifar | cifar10.py | Python | mit | 15,056 | [
"Gaussian"
] | 5c67f08e07a4e309cfd83986db3dbefbf120a3a1c6936c502376451a8bd611bd |
import msmbuilder.cluster, msmbuilder.msm, msmbuilder.example_datasets, msmbuilder.lumping, msmbuilder.utils
from sklearn.pipeline import make_pipeline
import mdtraj as md
n_micro = 750
#trajectories = [md.load("./trajectory%d.xtc" % i, top="./protein.pdb") for i in [1, 2]]
#trajectories = msmbuilder.example_datasets... | kyleabeauchamp/Caliber | src/cluster_new.py | Python | gpl-2.0 | 922 | [
"MDTraj"
] | aac7f91d24b374248a3372219e7c039d57fd29a4cb6ee2cbc42804def6334fcb |
#!/usr/bin/env python
"""
Artificial Intelligence for Humans
Volume 2: Nature-Inspired Algorithms
Python Version
http://www.aifh.org
http://www.jeffheaton.com
Code repository:
https://github.com/jeffheaton/aifh
Copyright 2014 by Jeff Heaton
Licensed under the Apache License, Versi... | PeterLauris/aifh | vol2/vol2-python-examples/examples/capstone_alife/run_milestone1.py | Python | apache-2.0 | 1,032 | [
"VisIt"
] | a711299d0a430d35dacf8e7828f66ad3c8373fb6621c291b3b77cf19c24defa1 |
"""
Parameterizes molecules for molecular dynamics simulations
"""
__version__ = '2.7.12'
__author__ = 'Robin Betz'
# Currently supported forcefields and information
supported_forcefields = {
"charmm": "CHARMM36m, July 2018 update",
"amber": "AMBER 14",
"opls": "OPLS AA/M, 2001 aminoacid dihedrals",
}
su... | Eigenstate/dabble | dabble/param/__init__.py | Python | gpl-2.0 | 1,426 | [
"Amber",
"CHARMM",
"Gromacs",
"LAMMPS"
] | aa6b9708f16fd59434f195d9b3a62cde35d98b18391bcf87a17669ca93c412a2 |
# Copyright (c) 2003-2010 LOGILAB S.A. (Paris, FRANCE).
# Copyright (c) 2009-2010 Arista Networks, Inc.
# http://www.logilab.fr/ -- mailto:contact@logilab.fr
# 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
# ... | dbbhattacharya/kitsune | vendor/packages/pylint/checkers/base.py | Python | bsd-3-clause | 30,316 | [
"VisIt"
] | da2d6c402385bd1796921d3fca369c853ade89148b59653dfa7203bc84759614 |
from . import config
from . import utils
from . import core
from . import io
from .external import Structure
from .core import *
from .DFT import *
from .Abinit import *
from .utils import *
from .flows import *
| trangel/OPTpy | OPTpy/__init__.py | Python | gpl-3.0 | 213 | [
"ABINIT"
] | fa4c698f19383e40a5e4392091b28f3df58ed7120955203c96a98cc122d66b10 |
"""
=================
Lorentzian Fitter
=================
"""
from __future__ import print_function
import numpy
from numpy.ma import median
from numpy import pi
from ...mpfit import mpfit
from . import fitter
from astropy.extern.six.moves import xrange
class LorentzianFitter(fitter.SimpleFitter):
def __init__():... | e-koch/pyspeckit | pyspeckit/spectrum/models/lorentzian.py | Python | mit | 1,941 | [
"Gaussian"
] | 5fad526e84854b14f58a85d79c1e1e3f76cc522865f5b9270b05152de0f2152a |
__author__ = 'Victoria'
#from src.game.Creature import *
from src.common.Observable import *
from src.game.Room2 import *
from src.game.StatePattern4 import *
from random import *
class Monster(Observable, Observer, Room):
def __init__(self, name):
super(Monster, self).__init__()
self._name = name
... | victorianorton/SimpleRPGGame | src/game/Monsters2.py | Python | mit | 2,335 | [
"VisIt"
] | 4485f4318465f834d8c568346a4f90a4780e7d7e9b5ce90a2c5cb327171f3f93 |
# Functions for a modified version of the PhiGs algorithm
# http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1523372/
# (We've added the use of synteny)
import sys,numpy,random
from scipy.signal import find_peaks
from . import trees,scores
from .Family import *
from .analysis import printTable
#### Main function
def creat... | ecbush/xtrans | xenoGI/families.py | Python | gpl-3.0 | 42,255 | [
"BLAST"
] | 9a6dcbf4d42f6a7f8f6f60bb5385deab8b1de9c157fd7f50ee7d0f4bdacfe5c0 |
"""Ladybug configurations.
Import this into every module where access configurations are needed.
Usage:
from ladybug.config import folders
print(folders.default_epw_folder)
folders.default_epw_folder = "C:/epw_data"
"""
import os
import json
class Folders(object):
"""Ladybug folders.
Args:
... | ladybug-analysis-tools/ladybug-core | ladybug/config.py | Python | gpl-3.0 | 5,373 | [
"EPW"
] | 5d0c0c5c185ed65909993600d9532a75aa6fd9f574c5de020224d0ef0050994b |
#import director
from director import cameraview
from director import transformUtils
from director import visualization as vis
from director import objectmodel as om
from director.ikparameters import IkParameters
from director.ikplanner import ConstraintSet
from director import polarisplatformplanner
from director imp... | patmarion/director | src/python/director/coursemodel.py | Python | bsd-3-clause | 5,177 | [
"VTK"
] | 9b95dd00305e27ac1075bb3959b001d625df1f6c4284219e9bee1c0f1c6e9bdb |
# Name: mapper_occci_online.py
# Purpose: Nansat mapping for OC CCI data, stored online in THREDDS
# Author: Anton Korosov
# Licence: This file is part of NANSAT. You can redistribute it or modify
# under the terms of GNU General Public License, v.3
# http://www.gnu.o... | nansencenter/nansat | nansat/mappers/mapper_opendap_osisaf.py | Python | gpl-3.0 | 3,073 | [
"NetCDF"
] | 2e9afb977b021248aaf61e131e59b8e0b61be05caf45f67647d8fba062d00cf7 |
import numpy as np
import unittest
import discretize
try:
import vtk.util.numpy_support as nps
except ImportError:
has_vtk = False
else:
has_vtk = True
if has_vtk:
class TestTensorMeshVTK(unittest.TestCase):
def setUp(self):
h = np.ones(16)
mesh = discretize.TensorMes... | simpeg/discretize | tests/base/test_tensor_vtk.py | Python | mit | 1,428 | [
"VTK"
] | e4eda4b2b8f2e5c35b48f8208592a53dbaa9afb94c5e638e145938d51062d9d8 |
# -*- coding: utf-8 -*-
# Copyright 2013 splinter authors. All rights reserved.
# Use of this source code is governed by a BSD-style
# license that can be found in the LICENSE file.
try:
import __builtin__ as builtins
except ImportError:
import builtins
import unittest
from imp import reload
from splinter.ex... | bmcculley/splinter | tests/test_browser.py | Python | bsd-3-clause | 1,746 | [
"VisIt"
] | f1b1d915fdd753f4eaad7dfe6752f726e89a64cc369d82ee76e9a72f8aa13cce |
from pymol.wizard import Wizard
from pymol import cmd
import pymol
import types
import string
class Pseudoatom(Wizard):
def __init__(self,mode='label',pos='[0.0,0.0,0.0]',_self=cmd):
Wizard.__init__(self,_self)
self.mode = mode
if mode == 'label':
self.prefix = 'Label text: \8... | gratefulfrog/lib | python/pymol/wizard/pseudoatom.py | Python | gpl-2.0 | 1,382 | [
"PyMOL"
] | 92249308d75554aefebf68310e21c8f73e71dcf2e7e3abfd13a35747be697c9f |
class WaterVapor(object):
"""
Vapor of H2O.
Note that the class name is singular.
"""
pass
class IceCrystal(object):
"""
Crystal of Ice.
Note that between classes there are always two spaces.
"""
pass
class SnowFlake(object):
""" Snowflakes. """
def __init__(self, ... | dokterbob/slf-programming-workshops | examples/snowball/water/phases.py | Python | mit | 433 | [
"CRYSTAL"
] | fea31d377b863dc09ae444664d5203edbda037f279a1afa646c42102d5ce28d0 |
# This file contains all functions to extract fundus curves from per-vertex-value (e.g., curvature) map
# Last updated: 2011-08-09 Forrest Sheng Bao
from mindboggle.utils import io_file, io_vtk, freesurfer
import libbasin
#import libfundifc as libskel
from numpy import mean, std, abs, matrix, zeros, flatnonzero, sign,... | binarybottle/mindboggle_sidelined | fundi_from_pits/libfundi.py | Python | apache-2.0 | 39,768 | [
"Gaussian",
"VTK"
] | de6c32d3f5ae96ce253ba8352e83c8ea15820c2f6a1ffff8f1621b435ec0db31 |
#! /usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Tests for the factor module in antitile.
"""
import unittest
import doctest
from operator import mul
from functools import reduce
from itertools import product
from antitile import factor
class TestFactor(unittest.TestCase):
def setUp(self):
self.domains... | brsr/antitile | tests/test_factor.py | Python | mit | 1,525 | [
"Gaussian"
] | 26745b715bc2eda4b035d8767ece5e0b12b709339c8c8f321e0c0254ed1b8426 |
"""User-friendly public interface to polynomial functions. """
from sympy.core import (
S, Basic, Expr, I, Integer, Add, Mul, Dummy,
)
from sympy.core.sympify import (
sympify, SympifyError,
)
from sympy.core.decorators import (
_sympifyit,
)
from sympy.polys.polyclasses import (
DMP, ANP, DMF,
)
f... | minrk/sympy | sympy/polys/polytools.py | Python | bsd-3-clause | 133,278 | [
"Gaussian"
] | 48385c7739953a8c2a3a1aaaf50ade9214fd6664d5bfdd988dccf5f5e6c48aa3 |
#!/usr/bin/env python
# This example demonstrates the generation of a streamsurface.
import vtk
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Read the data and specify which scalars and vectors to read.
pl3d = vtk.vtkMultiBlockPLOT3DReader()
pl3d.SetXYZFileName(VTK_DATA_ROOT +... | timkrentz/SunTracker | IMU/VTK-6.2.0/Examples/VisualizationAlgorithms/Python/streamSurface.py | Python | mit | 2,703 | [
"VTK"
] | 2aca9bc99ac5e4bde1329fd0701d8568f734cd1820cfb7b57ee6461634eaee3e |
# Copyright (C) 2018 Alex Nitz
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by the
# Free Software Foundation; either version 3 of the License, or (at your
# option) any later version.
#
# This program is distributed in the ho... | tdent/pycbc | pycbc/inference/models/single_template.py | Python | gpl-3.0 | 5,678 | [
"Gaussian"
] | bfa1e75343bafd4aac277b9c1119417a7b7f3cbeef3edd0a9f14563ef465f923 |
# -*- coding: utf-8 -*-
# <nbformat>3.0</nbformat>
# <headingcell level=1>
# Convert CNR Wave Data to NetCDF DSG (CF-1.6)
# <markdowncell>
# From Davide Bonaldo at CNR-ISMAR :
# here's a time series of wave data from Jesolo.
# * Columns 1 to 6: date (y m d h m s)
# * Column 7: Significant wave height (m)
# * Co... | rsignell-usgs/notebook | wave_data_to_netcdf.py | Python | mit | 2,702 | [
"NetCDF"
] | 5c26896e71aef8fb01f33d992932bfd14f97a397f70982274afc87b098ba477d |
#!/usr/bin/env python
#
# $File: reichEvolve.py $
#
# This file is part of simuPOP, a forward-time population genetics
# simulation environment. Please visit http://simupop.sourceforge.net
# for details.
#
# Copyright (C) 2004 - 2010 Bo Peng (bpeng@mdanderson.org)
#
# This program is free software: you can redistribut... | BoPeng/simuPOP | docs/reichEvolve.py | Python | gpl-2.0 | 2,263 | [
"VisIt"
] | c653b812a46729fe7121849d27166a816d60f22968c50c88d0d3992059020657 |
# (c) 2012-2014, Michael DeHaan <michael.dehaan@gmail.com>
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) an... | t0mk/ansible | lib/ansible/constants.py | Python | gpl-3.0 | 29,560 | [
"Galaxy",
"MOOSE"
] | 263d2ac7e769dd96b66b02f29fcb385a82249e2217d31bd34f509ae617be5fd5 |
"""\
CGBF.py Perform basic operations over contracted gaussian basis
functions. Uses the functions in PGBF.py.
References:
OHT = K. O-ohata, H. Taketa, S. Huzinaga. J. Phys. Soc. Jap. 21, 2306 (1966).
THO = Taketa, Huzinaga, O-ohata, J. Phys. Soc. Jap. 21,2313 (1966).
This program is part of the PyQuante qua... | gabrielelanaro/pyquante | PyQuante/CGBF.py | Python | bsd-3-clause | 7,318 | [
"Gaussian"
] | 9a7be6ec6b41614a0f613aa57dd2365963293ce0e4435c146168d32b0780d83f |
#!/usr/bin/python
#
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
# Copyright: (c) 2017 Gaurav Rastogi, <grastogi@avinetworks.com>
# GNU General Public License v3.0+ (see COPYING or https://www.gnu.org/licenses... | noroutine/ansible | lib/ansible/modules/network/avi/avi_sslprofile.py | Python | gpl-3.0 | 8,059 | [
"VisIt"
] | 882dc13968a262b66efe35877b2e76992f0644eaac17688ad6daaf67a2e43100 |
###########################################################################
#
# This program is part of Zenoss Core, an open source monitoring platform.
# Copyright (C) 2011, Zenoss Inc.
#
# This program is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License versi... | zenoss/ZenPacks.zenoss.PostgreSQL | ZenPacks/zenoss/PostgreSQL/parsers/__init__.py | Python | gpl-2.0 | 560 | [
"VisIt"
] | 7ff2ed461e41b204872862ffecf88d9ba49f8dd648044a12569b8f304c1aedb2 |
## begin license ##
#
# "CQLParser" is a parser that builds a parsetree for the given CQL and can convert this into other formats.
#
# Copyright (C) 2012-2013, 2020-2021 Seecr (Seek You Too B.V.) https://seecr.nl
# Copyright (C) 2021 Data Archiving and Network Services https://dans.knaw.nl
# Copyright (C) 2021 SURF htt... | seecr/cqlparser | test/speedtest.py | Python | gpl-2.0 | 4,059 | [
"VisIt"
] | fc3af1021d45f7792211ca30153f23185f1cbaf849099d5e23f627383288b608 |
"""
=============================================
SNR estimation for Diffusion-Weighted Images
=============================================
Computing the Signal-to-Noise-Ratio (SNR) of DW images is still an open
question, as SNR depends on the white matter structure of interest as well as
the gradient direction corr... | nilgoyyou/dipy | doc/examples/snr_in_cc.py | Python | bsd-3-clause | 6,592 | [
"Gaussian"
] | 14f9873b97a13754b1d65f2d3bdfbfd91c9054fba0c095569656d43ca6101f73 |
# coding=utf-8
# Copyright 2022 The Uncertainty Baselines Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by ap... | google/uncertainty-baselines | baselines/jft/experiments/imagenet21k_vit_l32_hetsngp.py | Python | apache-2.0 | 3,938 | [
"Gaussian"
] | 43aa758db9855dc00bf708bfde7b3fcd3406cd18776f46c33285fff666f1cc54 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
Classes for reading/manipulating/writing VASP ouput files.
"""
import json
import glob
import itertools
import logging
import math
import os
import re
import warnings
from pathlib import Path
import xml.et... | fraricci/pymatgen | pymatgen/io/vasp/outputs.py | Python | mit | 199,296 | [
"CRYSTAL",
"VASP",
"VisIt",
"pymatgen"
] | 71686ee9422ba96a77e38f0af25438a3a0a23435225c26b5b8f6eb5f2b9e3430 |
#
# Log-likelihood functions
#
# This file is part of PINTS (https://github.com/pints-team/pints/) which is
# released under the BSD 3-clause license. See accompanying LICENSE.md for
# copyright notice and full license details.
#
import pints
import numpy as np
import scipy.special
class AR1LogLikelihood(pints.Proble... | martinjrobins/hobo | pints/_log_likelihoods.py | Python | bsd-3-clause | 36,995 | [
"Gaussian"
] | d5ef51c606f6babcdb5b673120c3cfced0eeab42fe462f10a8e6bde53cd62250 |
# (C) British Crown Copyright 2010 - 2016, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | SusanJL/iris | lib/iris/tests/test_grib_save.py | Python | gpl-3.0 | 11,825 | [
"NetCDF"
] | e740d965d7f7fd069591fbdf7055469840b0a51374692ccdbb73de0923404540 |
# 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 version 2 of the Licens... | tuffy/python-audio-tools | audiotools/toc/__init__.py | Python | gpl-2.0 | 21,790 | [
"Brian"
] | be094c7f1f230e3abed8d39a27b87342f3440383c93ad2671389c71f1699d728 |
from .util import get_value_by_version, make_enum, OS_NAME
# base command
_simulation_base_command_matrix = {
"windows": {
(0, 0): "RunEPlus.bat",
(8, 2): "energyplus"
},
"osx": {
(0, 0): "runenergyplus",
(8, 2): "energyplus"
},
"linux": {
(0, 0): "bin/runene... | Openergy/oplus | oplus/compatibility/simulation.py | Python | mpl-2.0 | 1,958 | [
"EPW"
] | e60e318dbd09dc1b7e8edb481cddf52ff27bc4a4ca5f3506dbdee0bf123fcf1a |
#
# 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... | actuaryzhang/spark | python/pyspark/mllib/clustering.py | Python | apache-2.0 | 37,050 | [
"Gaussian"
] | 755850cd9bd722dbbcd74a0791edde1a83f3d8763ab8b3d52fe90e51922d1835 |
from datetime import datetime
from sqlalchemy import *
from sqlalchemy.orm import class_mapper
from turbogears import config
from turbogears.util import load_class
from turbogears.visit.api import BaseVisitManager, Visit
from turbogears.database import get_engine, metadata, session, mapper
import logging
log = loggi... | dockerera/func | funcweb/funcweb/identity/visit.py | Python | gpl-2.0 | 1,504 | [
"VisIt"
] | 7b13911fd5fca3f79aeb7be9ac284b00295eac25473d1662c23a00a7f2ab44b3 |
"""This demo solves the Stokes equations using an iterative linear solver.
Note that the sign for the pressure has been flipped for symmetry."""
# Copyright (C) 2010 Garth N. Wells
#
# This file is part of DOLFIN.
#
# DOLFIN is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser... | alogg/dolfin | demo/pde/stokes-iterative/python/demo_stokes-iterative.py | Python | gpl-3.0 | 2,955 | [
"VTK"
] | 1d81f05beefd369fa48dd2404be022d4561dd6dc74f0e233f943659a69ac9eaa |
import time
from watchdog.observers import Observer
from watchdog.events import FileSystemEventHandler, FileModifiedEvent
import sys
from subprocess import call
from splinter.browser import Browser
firefox = Browser()
class MdCompileHandler(FileSystemEventHandler):
def on_modified(self, event):
if isinsta... | andersoncardoso/small_scripts | landslide_presentation/python_brasil7/md_watchdog.py | Python | mit | 914 | [
"VisIt"
] | ededd203a3fdf75868c14b12e0704039f26d407bebbd256d222e9a1d66410554 |
#!/usr/bin/python
#
# Copyright 2015 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by... | imosquera/spinnaker | dev/build_release.py | Python | apache-2.0 | 24,397 | [
"ORCA"
] | da5abdfb498c50448f4aacb289922c944c57e01d4de5772a6aa7014ba23a15c7 |
# Copyright (c) 2006, 2008, 2010, 2013-2014 LOGILAB S.A. (Paris, FRANCE) <contact@logilab.fr>
# Copyright (c) 2014 Brett Cannon <brett@python.org>
# Copyright (c) 2014 Arun Persaud <arun@nubati.net>
# Copyright (c) 2015-2017 Claudiu Popa <pcmanticore@gmail.com>
# Copyright (c) 2015 Ionel Cristian Maries <contact@ionelm... | kczapla/pylint | pylint/pyreverse/utils.py | Python | gpl-2.0 | 6,238 | [
"VisIt"
] | ccc534240f093ee096a86bb554750bc008ab4a8f5e1a9324c70c54936c1c77c8 |
#
# @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
#... | jgonthier/psi4 | psi4/driver/driver_util.py | Python | lgpl-3.0 | 16,594 | [
"Psi4"
] | 331345c260eafdd4e62121806dd86a1722de03f1ea14d257788f20d45e7d2a34 |
#!/usr/bin/env python
# make index.html in results directory
import sys
from glob import glob
import os.path
from copy import deepcopy
import re
script, analysis_name, sample_csv_file, comparison_csv_file, output_dir, \
output_filename = sys.argv
# Output directories:
fastqc_dir = os.path.join(output_dir, "... | jessicachung/rna_seq_pipeline | scripts/html_index.py | Python | mit | 14,481 | [
"HTSeq"
] | feec37e984cfb7a26043a9e4089a24014879711f70e5eb32ff9a7e1d7fc1dae1 |
# 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 the G... | espressopp/espressopp | src/Int3D.py | Python | gpl-3.0 | 4,560 | [
"ESPResSo"
] | 06a394fae166f663200e216231dea303ce6b455b428e760a34b98d66efcc575a |
#!/usr/bin/env python
'''
Use multi-grid to accelerate DFT numerical integration.
'''
import numpy
from pyscf.pbc import gto, dft
from pyscf.pbc.dft import multigrid
cell = gto.M(
verbose = 4,
a = numpy.eye(3)*3.5668,
atom = '''C 0. 0. 0.
C 0.8917 0.8917 0.8917
... | sunqm/pyscf | examples/pbc/27-multigrid.py | Python | apache-2.0 | 1,230 | [
"PySCF"
] | 42d0450b8d9358af4199b46fd7512d86c1ff24493510c36020608b79c67ee45c |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# @Author: Brian Cherinka, José Sánchez-Gallego, and Brett Andrews
# @Date: 2016-04-11
# @Filename: rss.py
# @License: BSD 3-clause (http://www.opensource.org/licenses/BSD-3-Clause)
#
# @Last modified by: José Sánchez-Gallego (gallegoj@uw.edu)
# @Last modified time: 2018-... | sdss/marvin | python/marvin/tools/rss.py | Python | bsd-3-clause | 19,928 | [
"Brian"
] | 4ce6f356591ca20b6133442205a8fbd7f537fc3c83a0d03b807d610048b72f7b |
# coding: utf-8
from __future__ import unicode_literals
import re
from .common import InfoExtractor
from ..compat import compat_str
from ..utils import (
int_or_none,
parse_resolution,
str_or_none,
try_get,
unified_timestamp,
url_or_none,
urljoin,
)
class PeerTubeIE(InfoExtractor):
_... | spvkgn/youtube-dl | youtube_dl/extractor/peertube.py | Python | unlicense | 27,588 | [
"MOE"
] | 7e04d824aa63ed9be36e2368caa6f7314798528e3947d327b4dfa90f7768def2 |
#
# @file TestWriteSBML.py
# @brief Write SBML unit tests
#
# @author Akiya Jouraku (Python conversion)
# @author Ben Bornstein
#
# ====== WARNING ===== WARNING ===== WARNING ===== WARNING ===== WARNING ======
#
# DO NOT EDIT THIS FILE.
#
# This file was generated automatically by converting the file located a... | TheCoSMoCompany/biopredyn | Prototype/src/libsbml-5.10.0/src/bindings/python/test/sbml/TestWriteSBML.py | Python | bsd-3-clause | 56,577 | [
"VisIt"
] | 21001f09be8e6c3824ecb94f55192623d571066bbc450ad39a071d797a09aa7e |
import matplotlib.pyplot as plt
import numpy as np
from matplotlib.pyplot import Rectangle # Used to make dummy legend
# Open CSV File from Simulation
datafileS = open('../MASTER_DISTRIBUTIONS/HIIregion_popSynthesis.csv', 'r')
csvFileS = []
for row in datafileS:
csvFileS.append(row.strip().split(','))
# Save Galac... | WillArmentrout/galSims | tests/completeness/Completeness_TwoPanel_Compare_priortoJune4_2018.py | Python | gpl-2.0 | 25,987 | [
"Galaxy"
] | edebf7010b9b2200ee740c7d49b5b20b17a1a43ac5aa5178c348525276af5cd0 |
from setuptools import setup
setup(
name='moltemplate',
packages=['moltemplate',
'moltemplate.nbody_alt_symmetry'],
package_dir={'moltemplate': 'moltemplate'}, #.py files are in "moltemplate/"
package_data={'moltemplate': ['force_fields/*.lt']}, #.lt files are in "moltemplate/force_f... | smsaladi/moltemplate | setup.py | Python | bsd-3-clause | 4,935 | [
"ESPResSo",
"LAMMPS"
] | 2d7a16fffd11676f1d2ecd223aa3b2e0e8d53fec12fb0c9ade9604e895e26f28 |
# 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... | Lujeni/ansible | lib/ansible/galaxy/collection.py | Python | gpl-3.0 | 40,175 | [
"Galaxy"
] | eec1f1541776de2114535fea7cb3bcbd548481630eedac52c942910a3222cd75 |
# -*- coding: utf-8 -*-
#
# Copyright (C) University College London, 2013, all rights reserved.
#
# This file is part of FabMD and is CONFIDENTIAL. You may not work
# with, install, use, duplicate, modify, redistribute or share this
# file, or any part thereof, other than as allowed by any agreement
# specifically m... | uschille/FabSim | deploy/fabNanoMD.py | Python | lgpl-3.0 | 5,847 | [
"LAMMPS"
] | 921ea6c18cd3008394a08f3b1892baac86c28769c9c122e20e779eec391bf9fe |
from os.path import join
import os
import numpy as n
import glob
import sys
import time
import astropy.io.fits as fits
from os.path import join
import astropy.cosmology as co
cosmo = co.Planck13
import astropy.io.fits as fits
# for one galaxy spectrum
import GalaxySpectrumFIREFLY as gs
import StellarPopulationModel ... | JohanComparat/pySU | spm/bin_deep_surveys/create_summary_table_VVDS.py | Python | cc0-1.0 | 4,372 | [
"Galaxy"
] | 8c0e1b97505fe726f26194f1beaad2fd604745c52f614c523408284124aac062 |
from collections import OrderedDict
from .. import Provider as PersonProvider
class Provider(PersonProvider):
formats_female = OrderedDict((
('{{first_name_female}} {{last_name}}', 0.97),
('{{prefix_female}} {{first_name_female}} {{last_name}}', 0.015),
('{{first_name_female}} {{last_name... | danhuss/faker | faker/providers/person/en_US/__init__.py | Python | mit | 58,191 | [
"Amber",
"Brian",
"CRYSTAL",
"Dalton"
] | 78ce1a771922f819461c3a2e5ab451f511e1d10fa7506c2abe9022d1c68924fc |
#* This file is part of the MOOSE framework
#* https://www.mooseframework.org
#*
#* All rights reserved, see COPYRIGHT for full restrictions
#* https://github.com/idaholab/moose/blob/master/COPYRIGHT
#*
#* Licensed under LGPL 2.1, please see LICENSE for details
#* https://www.gnu.org/licenses/lgpl-2.1.html
"""Develope... | harterj/moose | python/MooseDocs/commands/check.py | Python | lgpl-2.1 | 4,072 | [
"MOOSE"
] | 48b9920dae42308955cd23b6bcc2cb91083f7285607514ca9611a6041121e03c |
"""
Performs depth-first search on the graph specified by infile and outputs the biconnected and strongly-connected
components.
"""
__author__ = 'Tom'
TREE, FORWARD, BACK, CROSS = 0, 1, 2, 3
class Node:
def __init__(self, value):
self.value = value
self.d = None
self.f = None
self... | tjtrebat/algorithms | algorithms/graph_algorithms/dfs/dfs.py | Python | gpl-2.0 | 5,205 | [
"VisIt"
] | 304f0744f839b802690f04b15acc780569a2bfd13ec9fa703af358fde331cf40 |
# Lint as: python3
# Copyright 2020 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless ... | tensorflow/docs | tools/tensorflow_docs/api_generator/report/linter.py | Python | apache-2.0 | 8,253 | [
"VisIt"
] | 069343620e66c931ca4421be29f96d30102cc1ec9cad5597da6e52941b440561 |
#!/usr/bin/env python
import os
import vtk
from vtk.test import Testing
from vtk.util.misc import vtkGetDataRoot
VTK_DATA_ROOT = vtkGetDataRoot()
# Image pipeline
reader = vtk.vtkMINCImageReader()
reader.SetFileName(VTK_DATA_ROOT + "/Data/t3_grid_0.mnc")
reader.RescaleRealValuesOn()
attributes = vtk.vtkMINC... | hlzz/dotfiles | graphics/VTK-7.0.0/IO/MINC/Testing/Python/TestMINCImageWriter.py | Python | bsd-3-clause | 1,971 | [
"VTK"
] | 2fbf378152fe563910070a74394d1f4e1bfef24eda6c18b6922461d7d8e3d626 |
#!/usr/bin/env python
# RegCM postprocessing tool
# Copyright (C) 2014 Aliou, Addisu, Kanhu, Andrey
# 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 Licens... | ansobolev/regCMPostProc | src/app.py | Python | gpl-3.0 | 2,109 | [
"NetCDF"
] | 66b14c7141840354d703580a4db499d88347e0880ce189f73706760d39088314 |
from questionnaire.models import Questionnaire, Section, SubSection, Question, QuestionGroup, QuestionOption, \
QuestionGroupOrder
questionnaire = Questionnaire.objects.get(name="JRF Core English", description="From dropbox as given by Rouslan")
section_1 = Section.objects.create(order=4, questionnaire=questionna... | eJRF/ejrf | questionnaire/fixtures/questionnaire/section_4a.py | Python | bsd-3-clause | 17,043 | [
"VisIt"
] | fb60a74be97373e1f41e50125d610177785a72f89d1195f3fe9664b29b3c6571 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
from pymatgen.analysis.elasticity.elastic import ElasticTensor
from pymatgen.analysis.interfaces.substrate_analyzer import SubstrateAnalyzer
from pymatgen.symmetry.analyzer import SpacegroupAna... | gmatteo/pymatgen | pymatgen/analysis/interfaces/tests/test_substrate_analyzer.py | Python | mit | 1,490 | [
"pymatgen"
] | e5f14b55d9a7ffb360087f08f9e0a215a7bd147e993d89f684264d14dd77d558 |
usage="""a module storing the methods to build priors.
print p[i]
This includes:
priors on strain decomposed into gaussian terms used in the analytic marginalization over all possible signals
priors on angular position, such as the galactic plane
"""
print """WARNING:
helpstrings are not necessarily accurate. U... | reedessick/bayesburst | priors.py | Python | gpl-2.0 | 39,548 | [
"Galaxy",
"Gaussian"
] | f4485cbb8b4d9bd5df9def180daa09ab801a4388d3b4958bada6fa7aa171a4ed |
#!/usr/bin/env python
# Copyright 2014-2018 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | gkc1000/pyscf | pyscf/scf/ucphf.py | Python | apache-2.0 | 5,875 | [
"PySCF"
] | 81c4fccbc9f07eea2840881150d97fc30f67bb549ae805e55a18d1c8a4da5a16 |
"""
@file
@brief Missing information about licenses
"""
missing_module_licenses = {
"xgboost": "Apache-2",
"actuariat_python": "MIT",
"code_beatrix": "MIT",
"ensae_teaching_cs": "MIT",
"pymyinstall": "MIT",
"pyensae": "MIT",
"pyquickhelper": "MIT",
"pymmails": "MIT",
"pyrsslocal": "... | sdpython/pymyinstall | src/pymyinstall/installhelper/missing_license.py | Python | mit | 12,065 | [
"Biopython",
"pymatgen"
] | 483c1b2be195f94b9f8742594d02a34cdef1e1004963ecb6a7ae5250381857e8 |
import numpy as np
from ase.structure import molecule
from ase.dft import Wannier
from gpaw import GPAW
from gpaw.test import equal
# Test of ase wannier using gpaw
calc = GPAW(gpts=(32, 32, 32), nbands=4)
atoms = molecule('H2', calculator=calc)
atoms.center(vacuum=3.)
e = atoms.get_potential_energy()
niter = calc.ge... | ajylee/gpaw-rtxs | gpaw/test/asewannier.py | Python | gpl-3.0 | 1,388 | [
"ASE",
"GPAW"
] | fe3ff238acb9ab9a6660f6b325fed75c4099682525b3c145defdb0d138bf228a |
"""Display the contents of the implementation cache."""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from __future__ import print_function
from zeroinstall import _
import os, sys
import gtk
from zeroinstall.injector import namespaces, model
from zeroinstall.z... | timdiels/0install | zeroinstall/gtkui/cache.py | Python | lgpl-2.1 | 23,076 | [
"VisIt"
] | 8bf40822b94e97113ebeaeb9cb88d82d6cc9c2ddf74f31d51b84fc63ea5da2c4 |
"""Module level filter."""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = '$Id$'
from DIRAC.FrameworkSystem.private.standardLogging.LogLevels import LogLevels
DOT = '.'
LEVEL = '__level__'
class ModuleFilter(object):
"""Filter module to set... | yujikato/DIRAC | src/DIRAC/Resources/LogFilters/ModuleFilter.py | Python | gpl-3.0 | 3,054 | [
"DIRAC"
] | 4cfa2c3bc7c5413199941017a60d23bd3c40f1a3deee4b531ffd12d16ce25d83 |
import ast
import datetime
import re
import secrets
import time
from datetime import timedelta
from typing import (
AbstractSet,
Any,
Callable,
Dict,
List,
Optional,
Pattern,
Sequence,
Set,
Tuple,
TypeVar,
Union,
)
import django.contrib.auth
from bitfield import BitField... | hackerkid/zulip | zerver/models.py | Python | apache-2.0 | 148,798 | [
"VisIt"
] | a0687008ccc3529961db98f545ed431aa0992d791097a11654864aae1baa2cae |
import pyspeckit
# Grab a .fits spectrum with a legitimate header
sp = pyspeckit.Spectrum('G031.947+00.076_nh3_11_Tastar.fits')
""" HEADER:
SIMPLE = T / Written by IDL: Tue Aug 31 18:17:01 2010
BITPIX = -64
NAXIS = 1 / number of array dimensions
NAXIS1 = 8192... | bsipocz/pyspeckit | examples/ammonia_vtau_fit_example.py | Python | mit | 2,881 | [
"Gaussian"
] | bf8301609de0681b225ae9df9baa956bba35e2c22d69f94633a28acc03d165e6 |
# Copyright 2007-2010 by Peter Cock. 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.
from __future__ import print_function
from Bio._py3k import basestring
import os
import war... | updownlife/multipleK | dependencies/biopython-1.65/Tests/test_SeqIO.py | Python | gpl-2.0 | 28,253 | [
"Biopython"
] | d4c6c480ca4b9bc92015ae37b552777984a77d2ab5da76f48006585671b73131 |
"""
========================================
Ammonia inversion transition TKIN fitter
========================================
Ammonia inversion transition TKIN fitter translated from Erik Rosolowsky's
http://svn.ok.ubc.ca/svn/signals/nh3fit/
.. moduleauthor:: Adam Ginsburg <adam.g.ginsburg@gmail.com>
Module API
^^^... | bsipocz/pyspeckit | pyspeckit/spectrum/models/ammonia.py | Python | mit | 34,486 | [
"Gaussian"
] | a0ce5c825c6c5f23e964a4aa09fa9f5c3baf1bcc8f3cef8768ec02e8ba62ce9a |
"""
pyDatalog
Copyright (C) 2012 Pierre Carbonnelle
Copyright (C) 2004 Shai Berger
This library is free software; you can redistribute it and/or modify
it under the terms of the GNU Lesser General Public License as
published by the Free Software Foundation; either version 2 of the
License, or (at your option... | baojie/pydatalog | pyDatalog/pyParser.py | Python | lgpl-2.1 | 37,914 | [
"VisIt"
] | 0cc4cbb7532c693226d4065b0930e22f8174d14ead089dfe83f2297483af14f5 |
#! /usr/bin/python
from setuptools import setup
import sys
sys.path.append("support");
sys.path.append("support/yaraspell");
sys.path.append("interfaces/web/lib");
sys.path.append("interfaces/web/lib/paste");
sys.path.append("interfaces/web/lib/simlejson");
sys.path.append("interfaces/web/lib/okasha2");
sys.path.append... | linuxscout/mishkal | exe_setup.py | Python | gpl-3.0 | 10,480 | [
"Cytoscape"
] | 775ef2c270c71f7c05ab59b69853b4b7d2bb0cae4d698f8b0fc646229185681e |
#
# @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
#... | ashutoshvt/psi4 | psi4/extras.py | Python | lgpl-3.0 | 6,694 | [
"CFOUR",
"Psi4"
] | 5d551b1b7a593d067e041a87116b72e312c91691952dd7a08af55bd4bae48f8d |
from .visitor import NodeVisitor
from ._compat import iteritems
VAR_LOAD_PARAMETER = 'param'
VAR_LOAD_RESOLVE = 'resolve'
VAR_LOAD_ALIAS = 'alias'
VAR_LOAD_UNDEFINED = 'undefined'
def find_symbols(nodes, parent_symbols=None):
sym = Symbols(parent=parent_symbols)
visitor = FrameSymbolVisitor(sym)
for nod... | facelessuser/sublime-markdown-popups | st3/mdpopups/jinja2/idtracking.py | Python | mit | 9,185 | [
"VisIt"
] | 693af84eec360ae7bd8d70d8242aee6126e91db2bdae4752f017942231f30fd2 |
"""
Harris Corner Detection
functions:
cv2.
cornerHarris()
cornerSubPix()
corners - regions in image with large variation in intensity in all directions
detect by:
find difference in intensity for a displacement of (u, v) in all directions
E(u, v) = sum(wrt x,y) w(x, y) [I(x+u, y+v) - I(x, y)]^2
... | SSG-DRD-IOT/commercial-iot-security-system | opencv/tutorials/featureDetection/harris_corner/harris_corner.py | Python | mit | 2,344 | [
"Gaussian"
] | cf903d26a18bfaa5e4b7742efe33321cc95e4d539e6216770007a5970d73b7d7 |
#!/usr/bin/env python
# Copyright (C) 2013-2018 The ESPResSo project
# Copyright (C) 2012 Olaf Lenz
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either versio... | mkuron/espresso | src/config/featuredefs.py | Python | gpl-3.0 | 6,855 | [
"ESPResSo"
] | 9e03cb5af2ef30eb49de193330a9e4c081d85c4631d8db383590c78af942363b |
#!/usr/bin/env python3
"""
Copyright 2017 Jocelyn Falempe kdj0c@djinvi.net
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, cop... | kdj0c/onepagepoints | onepagepoints.py | Python | mit | 15,902 | [
"BLAST"
] | 7c149954a408cc9d5242b6365149c0f608e8b06dc9403e9e7728879f6fe13f20 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.conf import settings
from django.conf.urls import include, url
from django.conf.urls.static import static
from django.contrib import admin
from django.views.generic import TemplateView
urlpatterns = [
url(r'^$', TemplateView.as_view(templ... | aniketmaithani/testing-cookiecutter | config/urls.py | Python | bsd-3-clause | 1,242 | [
"VisIt"
] | 523816d52d257718957437ef61dc4a9cacc4e3e2d84e146ed3d6705435b7a317 |
#!/usr/bin/env python3
import os
from setuptools import setup
def version():
setupDir = os.path.dirname(os.path.realpath(__file__))
versionFile = open(os.path.join(setupDir, 'checkm', 'VERSION'))
return versionFile.readline().strip()
setup(
name='checkm-genome',
version=version(),
author='Don... | Ecogenomics/CheckM | setup.py | Python | gpl-3.0 | 1,246 | [
"pysam"
] | 7802f332f6980ebec1d54ebf8c373982611b79697607bce54495773f3e1305e3 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | magic/tools/fitting.py | Python | agpl-3.0 | 24,098 | [
"Gaussian"
] | 383f19020db8a04b7833942cc15c7dd1b8fe1228c0f162bfc84d1d07885ad7b3 |
from unittest import TestCase
import macaroonbakery.httpbakery as httpbakery
import macaroonbakery.bakery as bakery
class TestWebBrowserInteractionInfo(TestCase):
def test_from_dict(self):
info_dict = {
'VisitURL': 'https://example.com/visit',
'WaitTokenURL': 'https://example.com... | go-macaroon-bakery/py-macaroon-bakery | macaroonbakery/tests/test_httpbakery.py | Python | lgpl-3.0 | 1,292 | [
"VisIt"
] | 4c53ce01afb7e55ae7d0c2c4be2b6696599b885b4c86a183826807f5009addde |
from __future__ import division, absolute_import, print_function
import warnings
import sys
import collections
import operator
import numpy as np
import numpy.core.numeric as _nx
from numpy.core import linspace, atleast_1d, atleast_2d
from numpy.core.numeric import (
ones, zeros, arange, concatenate, array, asarr... | LumPenPacK/NetworkExtractionFromImages | osx_build/nefi2_osx_amd64_xcode_2015/site-packages/numpy_1.11/numpy/lib/function_base.py | Python | bsd-2-clause | 144,305 | [
"Gaussian"
] | 5fa0c353b60947256018dc95d7d9c78d96d3a6e1c20dc83dd550a46b54e67cf4 |
"""
Created on June 18, 2015
@author: shiruilu
Common utils for CAPE
"""
import cv2
import numpy as np
from scipy.signal import argrelextrema
import matplotlib.pyplot as plt
def safe_convert(x, new_dtype):
"""
http://stackoverflow.com/a/23325108/2729100
convert x to new_dtype, clip values larger than max... | shiruilu/CAPE | cape_util/cape_util.py | Python | mit | 4,184 | [
"Gaussian"
] | d153138412baa3ef7b9588502c5b8bc50483d5f16c81dbb48017d1d2f49bf839 |
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