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# Licensed under a 3-clause BSD style license - see LICENSE.rst
# This module implements the base CCDPROC functions
from __future__ import (absolute_import, division, print_function,
unicode_literals)
import numbers
import numpy as np
from astropy.extern import six
from astropy.units.quantity ... | crawfordsm/ccdproc | ccdproc/core.py | Python | bsd-3-clause | 41,481 | [
"Gaussian"
] | 6ca09e8e7a77af3a428133b59c2e0832a0559fc2b951bebf2742f89c1e69906b |
__all__ = ['TreekvParser']
class Logger(object):
def __init__(self):
pass
def write(self, message):
print(message)
class KeyValue(object):
def __init__(self, key, value=None, lineinfo=None, logger=Logger()):
self.key = key
self.value = value
self._list = []
... | mizuy/seqtool | seqtool/util/parser.py | Python | mit | 6,396 | [
"Brian"
] | c27844eea78d0114770b87ee7f8db5568e282c182de5b8fb1d00e93cec07824a |
# Open Weather data file
#
# Ladybug: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Ladybug.
#
# Copyright (c) 2013-2015, Mostapha Sadeghipour Roudsari <Sadeghipour@gmail.com>
# Ladybug is free software; you can redistribute it and/or modify
# it... | boris-p/ladybug | src/Ladybug_Open EPW Weather File.py | Python | gpl-3.0 | 1,873 | [
"EPW"
] | 57909e37c4abb4a90209dcd6318539f43c5bc0b30f75a4fd90ac32e0e89dbdb6 |
#!/usr/bin/env python
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2018 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 redistri... | amjames/psi4 | psi4/share/psi4/fsapt/fsaptdiff.py | Python | lgpl-3.0 | 4,127 | [
"Psi4"
] | 12f2c22f38e11cf7537c1671a0f605e2f397bddf2140567e981a087e90302cfe |
from __future__ import unicode_literals
import functools
import os
import sys
import re
import git
import errno
import urllib3
import collections
import six
import platform
import txclib
try:
from json import loads as parse_json
except ImportError:
from simplejson import loads as parse_json
try:
import con... | transifex/transifex-client | txclib/utils.py | Python | gpl-2.0 | 23,720 | [
"VisIt"
] | c54aba80cae1d9e64ece84fa067c47d48c69213625f85e22ffbeb7e9664779da |
# -*- coding: utf-8 -*-
#
# Copyright (C) 2009,2013 Red Hat, Inc.
# This file is part of python-fedora
#
# python-fedora 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 2.1 of the Lice... | vivekanand1101/python-fedora | fedora/tg/identity/soprovidercsrf.py | Python | gpl-2.0 | 19,796 | [
"VisIt"
] | 3b8abd8c7d0fef8147fa0050ba85b6b7701ec29249c052ba906528b9e611b7ac |
# -*- coding: utf-8 -*-
"""
The MIT License (MIT)
Copyright (c) 2017 SML
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... | Dino0631/RedRain-Bot | cogs/notinusecogs/misc3.py | Python | gpl-3.0 | 68,662 | [
"CASINO"
] | 78bb9be71be22db7b953f14688751ac771b9b3c8ec7d0f8a2f042a35a6df8414 |
# Michael Christoffersen
# Script to perform supervised and unsupervised classification on
# multiband rasters, probably best used as a template for your own
# specific purpose
# Python 2.7
# GDAL ...
# Numpy ...
# SpectralPy ...
# PIL ...
from osgeo import gdal
from gdalconst import *
import numpy as np
import spec... | mchristoffersen/landuse | classify.py | Python | mit | 3,871 | [
"Gaussian"
] | 7741fc1ec407fc9f2a694368e5c3491827a814b7d0253fcaa7a803085fa27727 |
"""
xparm.py
(c) RIKEN 2015. All rights reserved.
Author: Keitaro Yamashita
This software is released under the new BSD License; see LICENSE.
"""
import numpy
from xds import get_xdsinp_keyword
from util import safe_float
class XPARM:
def __init__(self, xparm_file=None):
if xparm_file is not None:
... | keitaroyam/yam_scripts | xparm.py | Python | bsd-3-clause | 9,153 | [
"CRYSTAL"
] | 0ae93a434299109d3101e8e3d7e3d2dfeff69937a5f1e9d7b667da05313c6a97 |
################################################################################
# Peach - Computational Intelligence for Python
# Jose Alexandre Nalon
#
# This file: optm/sa.py
# Simulated Annealing
################################################################################
# Doc string, reStructuredText formatt... | anki1909/peach | peach/optm/stochastic.py | Python | lgpl-2.1 | 2,601 | [
"Gaussian"
] | cd564aa0b3dbccb88ea233b164ed1f82cf83f2ad3e9621134f2ca84ed7300f5d |
import os
import codecs
from setuptools import setup
from unslashed import __version__
here = os.path.abspath(os.path.dirname(__file__))
# Get the long description from the relevant file
with codecs.open(os.path.join(here, 'DESCRIPTION.rst'), encoding='utf-8') as f:
long_description = f.read()
setup(
name='d... | dghubble/django-unslashed | setup.py | Python | mit | 2,094 | [
"Dalton"
] | 15930b673d39ef788452f3630d4f63b689940cc457853f1b35fe3c88c6b8f84c |
import json
import os
from shutil import rmtree
from django.http import HttpResponse
from django.contrib.auth.models import User
from .models import DataFile, DataSet, DataType
from django.views.decorators.csrf import csrf_exempt
from local_settings import userdata_storage_path
def get_data_set_list(request):
"""... | sterlingbaldwin/acme_workbench | workbench-backend/file_manager/views.py | Python | bsd-2-clause | 7,137 | [
"NetCDF"
] | dee4f8f172bc1825e7ade7930203e54515d13161a37da744b54367e1bb6cb99a |
"""
**hep_ml.commonutils** contains some helpful functions and classes
which are often used (by other modules)
"""
from __future__ import print_function, division, absolute_import
from multiprocessing.pool import ThreadPool
import numbers
import itertools
import numpy
import pandas
from scipy.special import expit
tr... | chrinide/hep_ml | hep_ml/commonutils.py | Python | apache-2.0 | 13,648 | [
"Gaussian"
] | f7c3b143a6a1d93f2e3c52e366ac99cfe744016e9a7edc1b3aef99c642f79aff |
"""Map making from driftscan data using the m-mode formalism."""
import numpy as np
from caput import mpiarray, config
from ..core import containers, task, io
from ..util import tools
class BaseMapMaker(task.SingleTask):
"""Rudimetary m-mode map maker.
Attributes
----------
nside : int
Reso... | radiocosmology/draco | draco/analysis/mapmaker.py | Python | mit | 9,114 | [
"Gaussian"
] | a4025c101fdff1176412c7beb5e638381185c4041d088c82034fb700308b3037 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2012 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## 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 Foundati... | tiagocardosos/stoq | stoqlib/gui/test/test_paymentflowhistorydialog.py | Python | gpl-2.0 | 2,189 | [
"VisIt"
] | 6f462856036fccf6576bcb6936ab20fc63595a22cc5132e80a48bdf866fb1c31 |
#Python script to analyze dihedrals. Usage: "python dihedral_analyze.py (list of files to plot). D. Mobley, 5/16/07"
from numpy import *
from matplotlib import *
import sys
import re
from optparse import OptionParser
import os
import gzip
from scipy.stats import gaussian_kde
import matplotlib.pyplot as plt
from rstyle... | chris-lee-mc/MutInf | dihedral_analyze_compare.py | Python | gpl-3.0 | 28,220 | [
"Gromacs"
] | d3cedd17a15736e6ebae0adf9b33bbeba35491017e11e26905bad6c95a958407 |
import getpass
import itertools as it
import os
import collections as col
import numpy as np
import yaml
from lammps import lammps
import Save
import Tools
import helpers.git as _git
import helpers.sim_list
from Tools import lmp_control
__git_hash__ = _git.get_git_hash(__file__)
class Job(object):
def __init__(... | luminescence/PolyLibScan | job.py | Python | mit | 10,787 | [
"LAMMPS"
] | 88149b65449570af84718cfa0f4db0ce3839645fa7992aa79c177004988e80be |
#!/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
ANSIBLE_METADATA = {'metadata_version': '1.1',
... | e-gob/plataforma-kioscos-autoatencion | scripts/ansible-play/.venv/lib/python2.7/site-packages/ansible/modules/packaging/os/dpkg_selections.py | Python | bsd-3-clause | 2,142 | [
"Brian"
] | 08d98bb5bca85a5a0445d31e32366c91e2b87176e56015e7bfaa4ed3d7207e2e |
"""
*************** UTILITIES MODULE *******************
Generic functions to be used across multiple programs
within ALIAS.
***********************************************************
Created 24/11/2016 by Frank Longford
Contributors: Frank Longford
Last modified 27/2/2018 by Frank Longford
"""
import os
import n... | franklongford/alias | alias/src/utilities.py | Python | bsd-2-clause | 2,806 | [
"MDTraj"
] | 4e5d9b368e0d3f2c7f211b85bdc02eddf789a30f7c8fbeb661d892cb8b463841 |
"""
A collection of some useful ocean functions. These are taken from a range of
MATLAB toolboxes as well as from ocean_funcs.ncl, which in turn has taken them
from the CSIRO SEAWATER (now GSW) MATLAB toolbox.
The NCL code can be found at:
http://www.ncl.ucar.edu/Support/talk_archives/2013/att-1501/ocean_funcs.ncl... | pwcazenave/PyFVCOM | PyFVCOM/ocean.py | Python | mit | 41,266 | [
"NetCDF"
] | e1ce4ca70a6da4560ba818dde6823a5cb0f4716acfb72354e51efc3944658dcc |
#!/usr/bin/env python
#
# Author: Qiming Sun <osirpt.sun@gmail.com>
#
'''
A simple example to run CISD calculation.
'''
import pyscf
mol = pyscf.M(
atom = 'H 0 0 0; F 0 0 1.1',
basis = 'ccpvdz')
mf = mol.HF().run()
mycc = mf.CISD().run()
print('RCISD correlation energy', mycc.e_corr)
mf = mol.UHF().run()
m... | gkc1000/pyscf | examples/ci/00-simple_cisd.py | Python | apache-2.0 | 390 | [
"PySCF"
] | 2e6e9863abaf400d778f6d48415c0e55fb4a2a2927f48ab4c3c3bee1490dee5e |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
import glob
import os
import llnl.util.tty as tty
from spack import *
class GaussianSrc(Package):
"""Gaussian is a ... | LLNL/spack | var/spack/repos/builtin/packages/gaussian-src/package.py | Python | lgpl-2.1 | 5,182 | [
"Gaussian"
] | fd940cd5670da027e5643acbb89059f4ac07b795b3d96d71a97042fe7d943a44 |
from math import sqrt,log
import numpy as np
from matplotlib import pyplot
from spm1d import rft1d
eps = np.finfo(float).eps
def here_cca_single_node(y, x):
N = y.shape[0]
X,Y = np.matrix(x.T).T, np.matrix(y)
Z = np.matrix(np.ones(N)).T
Rz = np.eye(N) - Z*np.linalg.i... | 0todd0000/spm1d | spm1d/rft1d/examples/val_upx_4_X2_cluster.py | Python | gpl-3.0 | 2,865 | [
"Gaussian"
] | 5005cd1ad68a90f84888685d6715a2f789864201b66f4430de33603fe52685f3 |
from datetime import datetime, timedelta
import time
import random
import subprocess
import os
import os.path
import time
from collections import defaultdict
import json
import logging
import numbers
import yaml
from django.db import models
from django.contrib.auth.models import AbstractUser
import pexpect, getpass
i... | wolverton-research-group/qmpy | qmpy/computing/resources.py | Python | mit | 31,400 | [
"VASP"
] | f1096d8882e454ab1432bae8628587c4c2063c0de7a512e3a5229c159ed2ad4b |
import tkinter as tk
from tkinter import ttk
import matplotlib
from matplotlib import style
from PIL import Image, ImageTk
import time
import cv2 as cv2
large_font = ("Verdana", 12)
small_font = ("Verdana", 8)
ip = '10.54.65.58'
url1 = 'http://' + ip + ':5810/stream.mjpg'
class MainGui(tk.Tk):
def __init__(self... | SachinKonan/Windows-RPI-Vision-Framework | imageGrabTkinter.py | Python | mit | 3,722 | [
"VisIt"
] | 4c46867ac56b8461e72219391a31d98442b0fc610ef8ae6d97cb00ad8fa107fb |
"""
Test courseware search
"""
import json
from nose.plugins.attrib import attr
from common.test.acceptance.fixtures.course import CourseFixture, XBlockFixtureDesc
from common.test.acceptance.pages.common.auto_auth import AutoAuthPage
from common.test.acceptance.pages.common.logout import LogoutPage
from common.test.... | Stanford-Online/edx-platform | common/test/acceptance/tests/lms/test_lms_courseware_search.py | Python | agpl-3.0 | 7,754 | [
"VisIt"
] | 5d17ac979c6f4c432241c3b6274e4055c2638fb3356fd33e5e859fdaadb181e3 |
'''
C parser
'''
# Python imports
import re
from subprocess import Popen, PIPE
# clara lib imports
from .model import Var, Const, Op, Expr, VAR_IN, VAR_OUT, VAR_RET
from .parser import Parser, ParseError, addlangparser, NotSupported, ParseError
# Parser imports
from pycparser import c_ast, c_parser, plyparser
cla... | iradicek/clara | clara/c_parser.py | Python | gpl-3.0 | 20,983 | [
"VisIt"
] | 22a730ff8c7656d5320050a081e4f6db7782dd064b41ead8cd10dfdcf0dc51a8 |
# -*- coding: utf-8 -*-
# Author: Vincent Dubourg <vincent.dubourg@gmail.com>
# (mostly translation, see implementation details)
# Licence: BSD 3 clause
from __future__ import print_function
import numpy as np
from scipy import linalg, optimize
from ..base import BaseEstimator, RegressorMixin
from ..metrics... | valexandersaulys/airbnb_kaggle_contest | venv/lib/python3.4/site-packages/sklearn/gaussian_process/gaussian_process.py | Python | gpl-2.0 | 34,552 | [
"Gaussian"
] | 8a1f1eb96796cc4c4a41abf5489ed8144c9810bdb36b3f5e612b31be4824b058 |
# encoding:utf-8
"""
:synopsis: views diplaying and processing main content post forms
This module contains views that allow adding, editing, and deleting main textual content.
"""
import datetime
import logging
import os
import os.path
import random
import sys
import tempfile
import time
from django.shortcuts import ... | simalytics/askbot-devel | askbot/views/writers.py | Python | gpl-3.0 | 36,285 | [
"VisIt"
] | d09b6343767a75244f92072a78174adb50df6bf608ed310d945012eb2c44e80c |
# encoding: utf-8
"""
Autocall capabilities for IPython.core.
Authors:
* Brian Granger
* Fernando Perez
* Thomas Kluyver
Notes
-----
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2008-2011 The IPython Development Team
#
# Distributed under the terms of the BSD... | mattvonrocketstein/smash | smashlib/ipy3x/core/autocall.py | Python | mit | 1,974 | [
"Brian"
] | 9483c87c65da3cbb11edcf52e7b40608cbd90a994d9dce9ebe1d6b0fc7118ee2 |
#! /usr/bin/env python
# Authors: Vinu Vikraman <vvinuv@gmail.com>
from distutils.core import setup
setup(
name="kappabias",
version="0.1-dev",
description="Estimating bias from observed shear and galaxy distribution",
maintainer="Vinu Vikraman",
maintainer_email="vvinuv@gmail.com",
license="",... | vvinuv/kappabias | setup.py | Python | gpl-2.0 | 844 | [
"Galaxy"
] | adad5c94a63c7a70b864670240be23c554182b9873a44f58cbb64dac3237fadc |
# -*- coding: utf-8 -*-
"""Top-level display functions for displaying object in different formats.
Authors:
* Brian Granger
"""
#-----------------------------------------------------------------------------
# Copyright (C) 2013 The IPython Development Team
#
# Distributed under the terms of the BSD License. ... | noslenfa/tdjangorest | uw/lib/python2.7/site-packages/IPython/core/display.py | Python | apache-2.0 | 23,270 | [
"Brian"
] | 3f017b2bb377a8a2797c86c03263d03c10ee891c2604d2c92a939e5ab5112158 |
from ase import *
from gpaw import *
from gpaw.wavefunctions.pw import PW
from gpaw.xc.fxc import FXCCorrelation
from gpaw.test import equal
from gpaw.mpi import world, rank
from os import system
if world.size == 1:
scalapack1 = None
scalapack2 = None
elif world.size == 2:
scalapack1 = (2, world.size // 2,... | robwarm/gpaw-symm | gpaw/test/ralda_energy_H2.py | Python | gpl-3.0 | 2,176 | [
"ASE",
"GPAW"
] | 70ab488aba1fa8bd6a3a4e79247370d223ac74dde520d7a604dc450a2cc2e6a1 |
# Copyright (C) 2011-2012 CRS4.
#
# This file is part of Seal.
#
# Seal 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.
#
# Seal is dis... | crs4/seal | tests/tseal/lib/aligner/bwa/try_ann.py | Python | gpl-3.0 | 1,679 | [
"BWA"
] | a5759efc28e8716c745a4cba7b1ce8e8ff23dcdbd49c2b2fd54a501d31ac9f69 |
import vtk, sys, os
import numpy as np
class Scene3D:
"""A class to manage a 3D scene using VTK actors.
Each instance of this class has its own `vtkRenderer`, it can be used
to display the scene interactlively and/or save a still image in png
format. The actual 3D rendering is done by calling the `ren... | heprom/pymicro | pymicro/view/scene3d.py | Python | mit | 8,143 | [
"VTK"
] | 626bf568b59594653f4cd7c48dad7dd5ac14d0073d71dc87f6f63464b8be8bae |
#!/usr/bin/env python
'''
dirac-production-runjoblocal
Module created to run failed jobs locally on a CVMFS-configured machine.
It creates the necessary environment, downloads the necessary files, modifies the necessary
files and runs the job
Usage:
dirac-production-diracrunjoblocal (job ID) - No pare... | andresailer/DIRAC | TransformationSystem/scripts/dirac-production-runjoblocal.py | Python | gpl-3.0 | 5,276 | [
"DIRAC"
] | 28f1ee38401429fdff178d828a2b36e875ca54de68f6caf3d2357e108db45722 |
# -*- coding: utf-8 -*-
"""The config functions."""
# Authors: Eric Larson <larson.eric.d@gmail.com>
#
# License: BSD-3-Clause
import atexit
from functools import partial
import json
import os
import os.path as op
import platform
import shutil
import subprocess
import sys
import tempfile
import re
import numpy as np
... | mne-tools/mne-python | mne/utils/config.py | Python | bsd-3-clause | 21,498 | [
"VTK"
] | 045cc20d33b64935cede3e853fe3e632d08030b1524e7dda912c22652683716d |
"""
Downloads feeds, keys, packages and icons.
"""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _, NeedDownload
import os
from logging import info, debug, warn
from zeroinstall.support import tasks, basedir
from zeroinstall.injector.nam... | dabrahams/zeroinstall | zeroinstall/injector/fetch.py | Python | lgpl-2.1 | 18,271 | [
"VisIt"
] | 7dd74bad3f82b2c0c9f1e2f7f869b9cd7aab88c02a759afe39716e058745b575 |
# (C) British Crown Copyright 2014 - 2015, 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... | mo-g/iris | lib/iris/tests/unit/fileformats/netcdf/test_save.py | Python | gpl-3.0 | 3,049 | [
"NetCDF"
] | 2f9fb7283618a8b15fa0fa87915383ed5b1020fb83d72fa3503d11a2a321e6b2 |
# -*- coding: utf-8 -*-
"""
Created on Mon Sep 28 19:30:22 2015
@author: alex_
"""
# General Imports
import matplotlib as mpl
mpl.use('TkAgg') # Force mpl backend not to use qt. Else we have a conflict.
import numpy as np
#import pickle
import time
from datetime import datetime
#from collections import namedtuple
imp... | Alex-Ian-Hamilton/solarbextrapolation | solarbextrapolation/analyticalmodels/base.py | Python | mit | 8,490 | [
"Mayavi"
] | c74a08ea10c38eddc20f688c5b47e0ce5e02c57e2037ad567318eebf63ad34fc |
#! /usr/bin/env python
# -*- coding:utf-8
# Testing a deep neural network (multi layered perceptron model) with tensorflow.
# Special thanks: Harisson@pythonprogramming.net
'''
File name: neural_network_test.py
Author: chimney37
Date created: 11/03/2017
Python Version: 3.62
'''
import tensorflow as tf
... | chimney37/ml-snippets | neural_network_test.py | Python | mit | 6,353 | [
"NEURON"
] | 5c70861274451f70bc3fe2d1ac363ec17aedf0e09a0c37b1c4a373b9f637cece |
# -*- coding: iso-8859-1 -*
##
## (c) Fry-IT, www.fry-it.com, 2007
## <peter@fry-it.com>
##
"""
A very spartan attempt of a script that converts HTML to
plaintext.
The original use for this little script was when I send HTML emails out I also
wanted to send a plaintext version of the HTML email as multipart. Instead ... | erikdejonge/newsrivr | daemons/python2/html2plaintext.py | Python | gpl-2.0 | 5,926 | [
"VisIt"
] | c0d9c9c4e3972ffb5c8d6489154fc20202ae384e8213611b37bb745bef9b18ff |
import numpy as np
import pandas as pd
import mdtraj as md
filename = "./system.subset.pdb"
t = md.load(filename)
top, bonds = t.top.to_dataframe()
top.resSeq += (310 - 43 - 1) # Lose an extra 1 because PDB resSeq starts at 1, rather than zero
t._topology = md.Topology.from_dataframe(top, bonds)
t.save(filename)
... | hainm/MSMs | attic/src/code/hmsm/fix_pdb_resSeq.py | Python | gpl-2.0 | 1,020 | [
"MDTraj"
] | e4b9c44f42e4eb5c3c01efce83d33893eeb232f0b4cba344666637cd5834ae26 |
"""
Test script for building Python API for installing Galaxy tools using
CBL without any dependencies (i.e. it clones down CBL and utilizes it
like bcbio-nextgen's installer).
Goal is to ultimately fold something like this to Galaxy tool shed
client code to provide high-level support for easy CloudBioLinux based
tool... | heuermh/cloudbiolinux | deploy/test_install_galaxy_tool.py | Python | mit | 2,616 | [
"Galaxy"
] | 5b67b0c8ce83354b8ade8842f792734c0a8d371d2b20dcbdc8fdcea0d2f9dcef |
# -*- coding: utf-8 -*-
"""
ORCA Open Remote Control Application
Copyright (C) 2013-2020 Carsten Thielepape
Please contact me by : http://www.orca-remote.org/
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as publish... | thica/ORCA-Remote | src/ORCA/actions/AppControl.py | Python | gpl-3.0 | 22,327 | [
"ORCA"
] | 9a7e00efaf4e562cbd728651720dbe414b6dad575ca6b81bf53504dd6c53845d |
#!/usr/bin/env python
#
# $File: PyPenetrance.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 redistribu... | BoPeng/simuPOP | docs/PyPenetrance.py | Python | gpl-2.0 | 2,652 | [
"VisIt"
] | e0984ec165d5534ae65b19d31f4856d47a0442882caf6d6237e416ff8f9b62c8 |
#!/usr/bin/env python
try:
from math import inf
except ImportError:
inf = float("inf")
from argparse import ArgumentParser
import GetOrganelleLib
from GetOrganelleLib.pipe_control_func import *
from GetOrganelleLib.seq_parser import read_fasta, detect_plastome_architecture, DEGENERATE_BASES
import time
import... | Kinggerm/GetOrganelle | get_organelle_from_assembly.py | Python | gpl-3.0 | 70,992 | [
"BLAST"
] | d6c1388fe7605a1217d4350fa35cf2c25c8f2f78f0d25d8e82fcbf9fc32f8402 |
"""
@name: PyHouse_Install/src/Install/test/test_Utility.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2015 by D. Brian Kimmel
@license: MIT License
@note: Created on Oct 27, 2015
@Summary:
"""
# Import system type stuff
import unittest
# Import PyH... | DBrianKimmel/PyHouse_Install | src/Install/test/test_Utility.py | Python | mit | 551 | [
"Brian"
] | c0c8879dbfe4df047c873bf3e87028b04174ed17137a11777807e0ac0b1cee8e |
"""
Example of a demo that fits a Bayesian Gaussian Mixture Model (GMM)
to a dataset.
Variational bayes and Gibbs estimation are sucessively run on the same
dataset
Author : Bertrand Thirion, 2008-2009
"""
print __doc__
import numpy as np
import numpy.random as nr
import pylab as pl
import nipy.neurospin.cluster... | yarikoptic/NiPy-OLD | examples/neurospin/bayesian_gaussian_mixtures.py | Python | bsd-3-clause | 1,934 | [
"Gaussian"
] | 093a51904779dd351035788e516258b7d2d2a1c4c908a66d33325c788f73d94d |
# ----------------------------------------------------------------------
# Copyright (C) 2016, Numenta, Inc. Unless you have an agreement
# with Numenta, Inc., for a separate license for this software code, the
# following terms and conditions apply:
#
# This program is free software: you can redistribute it and/or mo... | rhyolight/NAB | nab/detectors/gaussian/windowedGaussian_detector.py | Python | agpl-3.0 | 3,320 | [
"Gaussian"
] | d711f66c1f269695bed9d43e7dd4190e9a001b75bd8eb97588ee6d854b4dbd7b |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Lee-Ping Wang
# Contributors: Robert McGibbon
#
# MDTraj is fr... | kyleabeauchamp/mdtraj | mdtraj/tests/test_arc.py | Python | lgpl-2.1 | 1,923 | [
"MDTraj"
] | 0d56d4b9a19ad96b42ba1487d3d6291ae90b34171d923b151c45409875641755 |
"""
This module contain solvers for all kinds of equations:
- algebraic or transcendental, use solve()
- recurrence, use rsolve()
- differential, use dsolve()
- nonlinear (numerically), use nsolve()
(you will need a good starting point)
"""
from __future__ import print_function, division
fr... | chaffra/sympy | sympy/solvers/solvers.py | Python | bsd-3-clause | 123,955 | [
"Gaussian"
] | 9abb39616d503f58efb3b9e6bfc5d7d1972e4fd6ba35ff4514e29c9049a28ac4 |
"""
CountModel class for dispatching different types of count models and different
types of estimation technqiues.
"""
__author__ = "Taylor Oshan tayoshan@gmail.com"
import numpy as np
from pysal.model.spglm.glm import GLM
from pysal.model.spglm.family import Poisson, QuasiPoisson
class CountModel(object):
"""
... | lixun910/pysal | pysal/model/spint/count_model.py | Python | bsd-3-clause | 7,328 | [
"COLUMBUS",
"Gaussian"
] | 1f3cfb3c32cb9724a4d821f694894d0bd3f59ba1bad87e4124a8d28100f7c5da |
"""
Contains a basic search interface for Galaxy
"""
import logging
from galaxy import web
from galaxy.web.base.controller import BaseUIController
log = logging.getLogger( __name__ )
class SearchController( BaseUIController ):
@web.expose
def index(self, trans):
return trans.fill_template( "search/in... | mikel-egana-aranguren/SADI-Galaxy-Docker | galaxy-dist/lib/galaxy/webapps/galaxy/controllers/search.py | Python | gpl-3.0 | 331 | [
"Galaxy"
] | da712799e68f14b39c3c5eb19b85bc383159f8c5c764d054ff6804f58318006d |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'user_frontend.ui'
#
# Created by: PyQt4 UI code generator 4.11.4
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
try:
_fromUtf8 = QtCore.QString.fromUtf8
except AttributeError:
def _fromUtf8... | kit-cel/gr-dab | python/GUI/user_frontend.py | Python | gpl-3.0 | 105,305 | [
"Galaxy"
] | 71046734f61728d8bcd6089bb84ed95ab96cda304337814a31beddab557a826b |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from __future__ import print_function
from __future__ import unicode_literals
if __name__ == '__main__':
import argparse
from Bio import AlignIO
from Bio.Align import MultipleSeqAlignment
from Bio.SeqRecord import SeqRecord
parser = argparse.Argument... | karolisr/krpy | krpy/tools/rename-seq-in-alignment.py | Python | gpl-3.0 | 1,775 | [
"Biopython"
] | 13963044ffc5984c75c6e8301b8ad3c52e820e9a0fbcf3bcc14e8bcae272ac3c |
# Copyright 2022 The Magenta Authors.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in ... | magenta/magenta | magenta/models/sketch_rnn/model.py | Python | apache-2.0 | 17,487 | [
"Gaussian"
] | 5e6e9f1fdc0b5458aad1c435ebeda5e7b848b07bd36339b8c45b9a7ffd0f992d |
import sys
from Bio.Blast import NCBIXML
def getHits(inputFile, evalue=0.01):
'''This function parses Blast output -- XML format
and reports a score for each match that has e-value less
than a given one or a default evalue (0.01).
The max score of each query is reported to stdout.
'''
queryWi... | likit/gimme | src/utils/blast_hits.py | Python | gpl-3.0 | 1,640 | [
"BLAST"
] | 69d6075de8565ff4ab9599b7cc611dfe7e27dbef2d90b4d82b1b12a4626ad764 |
# Copyright (C) 2010-2018 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... | hmenke/espresso | testsuite/python/engine_lbgpu.py | Python | gpl-3.0 | 3,833 | [
"ESPResSo",
"VTK"
] | 6ce2f3326a891c128f66c9bc3ffe1b08308916519d5f8ff872bf19254e72bf97 |
# Tested against Turbomole 7.4.1
import numpy as np
import pytest
from pysisyphus.benchmarks import Benchmark
from pysisyphus.calculators import Turbomole
from pysisyphus.cos.GrowingString import GrowingString
from pysisyphus.helpers import geom_loader
from pysisyphus.helpers_pure import eigval_to_wavenumber
from pys... | eljost/pysisyphus | tests/test_turbomole/test_turbomole.py | Python | gpl-3.0 | 4,100 | [
"TURBOMOLE"
] | 4be203ac3b1bf1ad68879c6f9807ab187329e73de2acb4b2fb6fb2b4d30b04b2 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import unittest
import os
from pymatgen.core.structure import Molecule
from pymatgen.io.xyz import XYZ
from pymatgen.io.vasp.inputs import Poscar
test_dir = os.path.join(os.path.dirname(__file__), "..", "..",... | gVallverdu/pymatgen | pymatgen/io/tests/test_xyz.py | Python | mit | 5,401 | [
"VASP",
"pymatgen"
] | b07290215d94e58a1c1a71e309d8ef9273fd19b376727c2261c9eb18e0fabfca |
from __future__ import absolute_import
import six
input_names = {'TL': '../examples/large_deformation/hyperelastic.py',
'UL': '../examples/large_deformation/hyperelastic_ul.py',
'ULM': '../examples/large_deformation/hyperelastic_ul_up.py'}
output_name_trunk = 'test_hyperelastic_'
from sfe... | rc/sfepy | tests/test_hyperelastic_tlul.py | Python | bsd-3-clause | 3,069 | [
"VTK"
] | 2d0984bbc4a70e6bdcea26f738f5ee4090904ef80f9c85ab4775aad855489e60 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# parser - General parser functions for jobs and resource confs
# Copyright (C) 2003-2013 The MiG Project lead by Brian Vinter
#
# This file is part of MiG.
#
# MiG is free software: you can redistribute it and/or modify
# it under the terms of the G... | heromod/migrid | mig/shared/parser.py | Python | gpl-2.0 | 28,790 | [
"Brian"
] | 465ab62f408a659418822208ee0ab821608124805863a331928e6389e4a98ff7 |
# Copyright (c) 2016 Jamie Bull
# Copyright (c) 2021 Johan Tibell
# Copyright (c) 2021 Dimitris Mantas
# =======================================================================
# Distributed under the MIT License.
# (See accompanying file LICENSE or copy at
# http://opensource.org/licenses/MIT)
# ===================... | santoshphilip/eppy | eppy/runner/run_functions.py | Python | mit | 12,557 | [
"EPW"
] | dc795a8b17955f9358e89bb8cd86cfcb56716d8418a0f2d31503e19dda5a4768 |
#!/usr/bin/env python
# -*- coding:utf-8 mode:python; tab-width:4; indent-tabs-mode:nil; py-indent-offset:4 -*-
##
"""
test_energy_semiempirical_gamess_us
~~~~~~~~~~~~~~
Test GAMESS-US implementations for semiempirical energy jobs.
"""
import sys
import geoprep
from adapters import gamess_us
from tests.c... | mattbernst/polyhartree | tests/test_energy_semiempirical_gamess_us.py | Python | gpl-3.0 | 2,431 | [
"GAMESS"
] | 82284173115213750182e03a6c8a978156fdd77cbcb7794981aa62499e83db89 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import unittest
from monty.os.path import which
import warnings
from pymatgen.ext.cod import COD
"""
Created on Jun 9, 2012
"""
__author__ = "Shyue Ping O... | czhengsci/pymatgen | pymatgen/ext/tests/test_cod.py | Python | mit | 1,304 | [
"pymatgen"
] | 92c747fc9db2a70b02c3312519c47001fadde6f4fd12a3e9c8428eeb1a4ddf00 |
# Copyright (c) 2017 the GPy Austhors (see AUTHORS.txt)
# Licensed under the BSD 3-clause license (see LICENSE.txt)
from ..core import Model
from ..core.parameterization import Param
from ..core import Mapping
from ..kern import Kern, RBF
from ..inference.latent_function_inference import ExactStudentTInference
from ..... | SheffieldML/GPy | GPy/models/tp_regression.py | Python | bsd-3-clause | 12,410 | [
"Gaussian"
] | ebef0e9b8452b530806d22594330f57e090cef1e0330f41d4a7770831a2fad99 |
import os
import sys
import subprocess
from setuptools import setup, find_packages, Command
datadir = 'deenurp/data'
version_file = f'{datadir}/version.txt'
subprocess.call(
(f'mkdir -p {datadir} && '
f'git describe --tags --dirty > {version_file}.tmp '
f'&& mv {version_file}.tmp {version_file} '
... | fhcrc/deenurp | setup.py | Python | gpl-3.0 | 2,726 | [
"Biopython"
] | 3e73b06cdaafc1aad1ef6176239ad398f8a2bf4b2284eb64669bdb8bab44a8f2 |
#!/usr/bin/env python
"""
bin_reads_into_genes.py
Author: Tony Papenfuss
Date: Tue 23 Feb 2010 21:30:42 EST
"""
import os, sys
from pysam import Samfile
# Input data
annoFilename = "/Users/papenfuss/databases/platypus/annotation/ensembl/Release54/mart_gene_location.txt"
fields = ["geneId", "chrom", "start", "end"... | PapenfussLab/Srtools | snippets/bin-reads-into-genes-using-sam.py | Python | artistic-2.0 | 1,637 | [
"pysam"
] | 98f4d2c2fc1c56de6c575c8fa1a82c7da32117ae1f3cdec957b7246ddfe99094 |
from OpenGL.GL import *
from OpenGL.GL.ARB.vertex_buffer_object import *
from pymol.callback import Callback
from pymol import cmd
# this is an example of creating a callback object which
# uses GL arrays. Requires Numeric Python:
from numpy import *
# define a callback object
class myCallback(Callback):
def _... | gratefulfrog/lib | python/pymol/pymol_path/examples/devel/gl03.py | Python | gpl-2.0 | 1,632 | [
"PyMOL"
] | cf60f9540141e89aaf7df860e1822d939aa9ac78edfcf8bb36f8af5319842a1b |
# -*- coding: utf-8 -*-
#
# precise_spiking.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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... | hakonsbm/nest-simulator | pynest/examples/precise_spiking.py | Python | gpl-2.0 | 5,236 | [
"NEURON"
] | 57f1f5234371e5b30bcb911fec5e189c7b7e3033758db81019c8284a77c45166 |
APP_NAME = "mvp_maternal_health"
MATERNAL_HEALTH_INDICATORS = dict(
app=APP_NAME,
indicators=dict(
pregnancy_danger_signs=dict(
pregnancy_visit_danger_sign=dict(
description="No. of Pregnant Women With Danger Sign Recorded During Visit",
title="# Pregnant Wom... | qedsoftware/commcare-hq | custom/_legacy/mvp/static_definitions/couch/maternal_health.py | Python | bsd-3-clause | 2,681 | [
"VisIt"
] | c3349fe1d5995c1d827cf82c50c7b10b3eb4f5d7bd168e209a4ce4b647ec1e01 |
from itertools import chain
try: # When this is imported in Kataja context
from Monorail2.Constituent import Constituent
from Monorail2.Feature import Feature
from kataja.syntax.SyntaxState import SyntaxState
from Monorail2.utils import simple_bracket_tree_parser
except ImportError: # this is ... | jpurma/Kataja | plugins/Monorail2/Parser.py | Python | gpl-3.0 | 9,594 | [
"VisIt"
] | 6e203ffbd0c29222e617daacf0a0cd0c3bc979f4c2f4fc7861ed91d6fcbae8e6 |
# Mantid Repository : https://github.com/mantidproject/mantid
#
# Copyright © 2018 ISIS Rutherford Appleton Laboratory UKRI,
# NScD Oak Ridge National Laboratory, European Spallation Source
# & Institut Laue - Langevin
# SPDX - License - Identifier: GPL - 3.0 +
from __future__ import (absolute_import, divi... | mganeva/mantid | Framework/PythonInterface/test/python/plugins/functions/StretchedExpFTTest.py | Python | gpl-3.0 | 1,778 | [
"Gaussian"
] | 79b1368083ff8f5460752178ef6eb89e4f8bf9ec2c15cab42e9fdfbd9c3e9771 |
# -*- coding: utf-8 -*-
'''auto filtering call chain test mixins'''
from inspect import ismodule
from twoq.support import port
class ASliceQMixin(object):
def test_first(self):
self.assertEqual(self.qclass(5, 4, 3, 2, 1).first().end(), 5)
def test_nth(self):
self.assertEqual(self.qclass(5,... | lcrees/callchain | callchain/tests/mixins/auto/filtering.py | Python | mit | 6,878 | [
"MOE"
] | 7f16bb6127910c61a28e12738a43de1d0a61cf5a5ed8f803bd684f2128e3e7ed |
# -*- coding: utf-8 -*-
"""
colorful
~~~~~~~~
Terminal string styling done right, in Python.
:copyright: (c) 2017 by Timo Furrer <tuxtimo@gmail.com>
:license: MIT, see LICENSE for more details.
"""
import ast
import os
import sys
import codecs
from setuptools import setup, find_packages
# These... | timofurrer/colorful | setup.py | Python | mit | 3,494 | [
"VisIt"
] | efb8864e002e3481e72dfcad7e54cb002ce4f5e7ee6a1f4a8907ee73276ebcb3 |
# -*- 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-dataplex | tests/unit/gapic/dataplex_v1/test_dataplex_service.py | Python | apache-2.0 | 368,853 | [
"Octopus"
] | a6b20a7415c79f34724539c7b39dc5a290bcc588046e27cb9e215978aa5b1c6e |
#!/usr/bin/python -u
import os, subprocess
from argparse import Namespace
import run_setup
from run_setup import WorkdirStructure
from gmx_engine import GmxEngine
from gmx_params import GmxParameters
#########################################
def make_xtc(params):
pdbname = params.run_options.pdb
xtc_file =... | ivanamihalek/smallmol | gmx_lib/postproduction.py | Python | gpl-2.0 | 5,080 | [
"Gromacs"
] | 51ad2aaf42c78c996bc67d9959f7f544d05699a15038b22dc868f66b9a78931d |
# $Id$
#
# Copyright (c) 2007-2013, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the ... | adalke/rdkit | Projects/DbCLI/SearchDb.py | Python | bsd-3-clause | 24,171 | [
"RDKit"
] | 641efb20d29d0fca5dd393c36aa432e58984d5790f8a5ca3b502bec6454dcf0b |
#!python
# coding=utf-8
import base64
import random
import string
import operator
import itertools
import simplejson as json
import numpy as np
import netCDF4 as nc4
from pyaxiom.urn import IoosUrn
from pyaxiom import logger
class DotDict(object):
def __init__(self, *args, **kwargs):
for k, v in kwargs.... | axiom-data-science/pyaxiom | pyaxiom/utils.py | Python | mit | 12,384 | [
"NetCDF"
] | b7d1bee2ec1c9e86fdfc43cdb5bfe52dc1eca41d5a100e49e010d071d2cd4053 |
#!/usr/bin/env python
#
# Copyright 2016 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 requir... | Aloomaio/googleads-python-lib | examples/adwords/v201802/campaign_management/add_complete_campaigns_using_batch_job.py | Python | apache-2.0 | 15,591 | [
"VisIt"
] | 861b76a3047d3d8d00a494145cb291e597cd26a83a8ff9ae8674a47bd7b7f103 |
# -*- coding: utf-8 -*-
from models.utils import UserVars
import numpy as np
from operator import mul
from numpy.linalg import inv
from geometry_modules import *
import domain_creator
"""functions in this class
adding_oxygen: add one molecule in the frame of spherical sphere (r, theta, phi should be specified)
add_oxy... | jackey-qiu/genx_pc_qiu | models/domain_creator_water.py | Python | gpl-3.0 | 24,459 | [
"CRYSTAL"
] | 502f1b3da8aa7bafa23890b42c457ab97d3aad16e2677f6d92c461ad70435b15 |
# Copyright (C) 2013,2014,2015,2016 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 version 3 of the L... | Marcello-Sega/espresso | src/core/gen_featureconfig.py | Python | gpl-3.0 | 3,818 | [
"ESPResSo"
] | 480ae4073cd97a63b17596edaeed596f871ad0aee78ecb2dfe4a129b60afe41a |
# -*- coding: utf-8 -*-
"""Copyright 2015 Roger R Labbe Jr.
FilterPy library.
http://github.com/rlabbe/filterpy
Documentation at:
https://filterpy.readthedocs.org
Supporting book at:
https://github.com/rlabbe/Kalman-and-Bayesian-Filters-in-Python
This is licensed under an MIT license. See the readme.MD file
for mo... | rlabbe/filterpy | filterpy/kalman/tests/ukf2.py | Python | mit | 47,471 | [
"Gaussian"
] | 71a675314507394f4606db8e2872b4480b5b71251dd90591efbf0b6b794b3fd7 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
#
# ePuck.py
#
# Copyright 2010 Manuel Martín Ortiz <mmartinortiz@gmail.com>
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; eit... | rezeck/epuck_driver | src/epuck/ePuck.py | Python | gpl-2.0 | 30,782 | [
"VisIt"
] | 022e907a775015921133b18eeac0d9085e7ecd52b082610fcfb0de60294a69cb |
from numpy.testing import *
from numpy import random
import numpy as np
class TestRegression(TestCase):
def test_VonMises_range(self):
"""Make sure generated random variables are in [-pi, pi].
Regression test for ticket #986.
"""
for mu in np.linspace(-7., 7., 5):
r = ... | dagss/numpy_svn | numpy/random/tests/test_random.py | Python | bsd-3-clause | 3,680 | [
"Gaussian"
] | 8c82bc1325577db9edf33129e8fccff598c69730aad737745075ec4ec67c5c77 |
#!/usr/bin/env python
import sys
extras = {}
try:
from setuptools import setup
extras['zip_safe'] = False
if sys.version_info < (2, 6):
extras['install_requires'] = ['multiprocessing']
except ImportError:
from distutils.core import setup
setup(name='futures',
version='2.1.4',
descr... | akrehl/dotfiles | vim/bundle/YouCompleteMe/third_party/pythonfutures/setup.py | Python | mit | 1,249 | [
"Brian"
] | 9b8cbf6f8b7aa781accea1414c6aaee457e8573e2199dd83c7301d489aafc827 |
from other.logger import *
def get_namespace(fac):
# DEVELOPERS DEVELOPERS DEVELOPERS DEVELOPERS DEVELOPERS DEVELOPERS
# DEVELOPERS DEVELOPERS DEVELOPERS DEVELOPERS DEVELOPERS DEVELOPERS
# DEVELOPERS DEVELOPERS DEVELOPERS DEVELOPERS DEVELOPERS DEVELOPERS
return \
'''from core.QueryManager import RawResu... | Erotemic/hotspotter | _graveyard/oldhotspotter/other/dev.py | Python | apache-2.0 | 2,048 | [
"EPW"
] | 1aa1a7877de90807275fe32866f314476d489b79259daa3b09c121aa900bc22c |
from __future__ import (division, absolute_import, with_statement,
print_function, unicode_literals)
from stix2 import v20
def create_stix2_bundle(objects):
'''
Creates a STIX2 Bundle object from a list of objects.
Args:
objects: list of ``stix2`` SDO objects.
Return... | mitre/multiscanner | multiscanner/common/stix2_generator/__init__.py | Python | mpl-2.0 | 9,890 | [
"VisIt"
] | f3c5bc7a7369c9c2b5173ea91b803e917e9b612f9f528fe6a1f587cb0d5e66aa |
# -*- coding: utf-8 -*-
import re
from south.utils import datetime_utils as datetime
from south.db import db
from south.v2 import DataMigration
from django.db import models
def whitespace_ignoring_equal(a, b):
def squash(x):
return re.sub('\s', '', x)
return squash(a) == squash(b)
old_mailit_text =... | TEDICpy/write-it | mailit/migrations/0008_update_mailit_message_templates.py | Python | gpl-3.0 | 14,956 | [
"VisIt"
] | e3f146449eb9fdb46f3d4ec2eb5f95e811ebc0eceb59778a3bf104fa1920919b |
'''
Random Field Theory expectations and probabilities.
The core RFT computations are conducted inside **prob.rft**, and the
**RFTCalculator** class serves as a high-level interface to **prob.rft**
'''
# Copyright (C) 2022 Todd Pataky
from math import pi,log,sqrt,exp
import numpy as np
from scipy import stats,op... | 0todd0000/spm1d | spm1d/rft1d/prob.py | Python | gpl-3.0 | 21,886 | [
"Gaussian"
] | 017a8da4317954c465af485759a578aea0fffec49cf09f1fa7ee2f2d074e3b42 |
"""
Optimade support.
"""
import logging
import sys
from collections import namedtuple
from os.path import join
from typing import Dict, List, Optional, Set, Union
from urllib.parse import urlparse
import requests
from tqdm import tqdm
from pymatgen.core.periodic_table import DummySpecies
from pymatgen.core.structur... | materialsproject/pymatgen | pymatgen/ext/optimade.py | Python | mit | 23,621 | [
"pymatgen"
] | d88fcc1b8d6003502d92981252c35fe15813d855928ef9bb9b7bae971b9ec59a |
# -*- 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/gapic-generator-python | tests/integration/goldens/asset/tests/unit/gapic/asset_v1/test_asset_service.py | Python | apache-2.0 | 158,421 | [
"Octopus"
] | 3b84472319dda110d25ef4246238f600ee20eb0845cd0f05243c6a42c7f8ae63 |
# -*- coding: utf-8 -*-
#
# urbanczik_synapse_example.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST 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 t... | tammoippen/nest-simulator | pynest/examples/urbanczik_synapse_example.py | Python | gpl-2.0 | 12,226 | [
"NEURON"
] | 839bffaec2f228db9fab32032b432a9202cae0b7d513d00f38799e3163189047 |
from __future__ import division, print_function, unicode_literals
"""
This module tests the combinatoric generation of compositions.
"""
__author__ = "Chuck-Hou Yee"
__copyright__ = "Copyright 2015, Correlated Materials Laboratory"
__version__ = "0.1"
__maintainer__ = "Chuck-Hou Yee"
__email__ = "chuckyee@physics.rut... | correlatedmaterialslaboratory/pymatdesign | pymatdesign/tests/test_design.py | Python | mit | 6,257 | [
"pymatgen"
] | 0d41d9d71b42af52b858e155efb151af7ba3771e96c1062905f6ee17f6eb0b80 |
# #
# Copyright 2012-2021 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 (... | hpcugent/easybuild-framework | test/framework/filetools.py | Python | gpl-2.0 | 162,322 | [
"NetCDF"
] | a7d1e6c81fa59307e48c2e11977e4dedae39c37f96b8894053f2942748947a9f |
########################################################################
# File : dirac-proxy-init.py
# Author : Adrian Casajus
###########################################################from DIRAC.Core.Base import Script#############
import sys
import getpass
import DIRAC
from DIRAC.Core.Base import Script
__RCS... | andresailer/DIRAC | FrameworkSystem/Client/ProxyUpload.py | Python | gpl-3.0 | 6,021 | [
"DIRAC"
] | fb7e9e8e70fc68d17503aa3cb9874c3a27da7282e87f11761b870b6afe81b196 |
# coding=utf-8
import os
import unittest
import numpy as np
from pkg_resources import resource_filename
from compliance_checker.base import BaseCheck, GenericFile, Result
from compliance_checker.suite import CheckSuite
static_files = {
"2dim": resource_filename("compliance_checker", "tests/data/2dim-grid.nc"),... | aodn/compliance-checker | compliance_checker/tests/test_suite.py | Python | apache-2.0 | 9,256 | [
"BWA",
"NetCDF"
] | a275ae9910fe3eef9e63542f7f9fde7515bc4bb392fad9ccaa724a38f248df05 |
#!/usr/bin/env python
# -*- coding=utf-8 -*-
"""
_ _ _____ _____ __ _ _____ _____
| | | | | _ \ / _ \ | \ | | | _ \ / ___/
| |_| | | |_| | | | | | | \| | | | | | | |___
| _ | | _ { | | | | | |\ | | | | | \___ \\
| | | | | |_| | | |_| | | | \ | | |_| | ___| |
|_| |_| |_____/ \_____/ |_... | gVallverdu/myScripts | GROMACS/hbonds.py | Python | gpl-2.0 | 18,791 | [
"Gromacs",
"MDTraj"
] | 27254786857c0e5344beb17f3b53cc67d99af529d71512e25f285a8a9b4c3feb |
#!/usr/bin/en python
import os
import sys
import glob
import json
import numpy as np
import pandas as pd
from lxml import objectify
def read_xml_sidecar(filepath):
"""
Read a CMTK xml sidecar file.
Returns
=======
lxml.objectify
"""
abs_path = os.path.abspath(filepath)
with open(abs_... | nicholsn/ncanda-data-integration | scripts/xnat/check_gradient_tables.py | Python | bsd-3-clause | 6,792 | [
"VisIt"
] | cef41db554be481440e22dff767a60d037a5902b8eb6e9ebb0e98d26e7b9eddf |
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