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#!/usr/bin/env python
'''unit testing code for pysam.
Execute in the :file:`tests` directory as it requires the Makefile
and data files located there.
'''
import sys
import os
import shutil
import gzip
import pysam
import unittest
import glob
import re
from TestUtils import checkBinaryEqual, checkGZBinaryEqual, check... | pysam-developers/pysam | tests/tabix_test.py | Python | mit | 40,992 | [
"pysam"
] | 8b5be24042def5e7c8f2e4e34fd2c3258d5a272e76c7c829e3a6dce36f018be2 |
# Copyright (C) 2007, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import os
from zeroinstall import SafeException
release_uri = 'http://0install.net/2007/interfaces/0release.xml'
umask = os.umask(0)
os.umask(umask)
def init_releases_directory(feed):
files = os.listdir('.')
if f... | 0install/0release | setup.py | Python | lgpl-2.1 | 1,998 | [
"VisIt"
] | af59c2755c31c929a7414cf8018aba3168ca113e0601c7f267501f797f4550f3 |
from __future__ import print_function
import unittest
from netcdf import netcdf as nc
from models import JobDescription
from models.cache import Cache, StaticCache
import os
import glob
class TestHeliosat(unittest.TestCase):
def setUp(self):
os.system('rm -rf static.nc product')
os.system('cp -rf... | gersolar/solar_radiation_model | tests/heliosat_test.py | Python | mit | 3,898 | [
"NetCDF"
] | 14c6351725f3090762daa6d0ce7f7aa67ef219f14bea0820d61c0e0069ea6251 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RPcamethods(RPackage):
"""A collection of PCA methods.
Provides Bayesian PCA, Prob... | iulian787/spack | var/spack/repos/builtin/packages/r-pcamethods/package.py | Python | lgpl-2.1 | 1,640 | [
"Bioconductor"
] | 44c1a40ba6023318cada4eccd7a0aae27884e1663854a2e6ffc8571f80edb588 |
#!/usr/bin/env python
# Copyright 2014-2020 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/tdscf/rks.py | Python | apache-2.0 | 9,576 | [
"PySCF"
] | db3e7a2637e6686ce66ff76d46ffa9a15688168e0a9a9b497e23a1944d9211fa |
"""
A standalone program to explore error model minimisation after scaling.
Scale factors and outliers determined from scaling are respected.
Profile intensities will be used by default. Profile/summation intensity
combination can be used, with the options:
intensity_choice=combine combine.Imid={value}
All scalin... | dials/dials | command_line/refine_error_model.py | Python | bsd-3-clause | 7,283 | [
"CRYSTAL"
] | b18167e2f055e4e93d19676067e8a2766771562f7e24f56e67dbcccfdb7725db |
#!/usr/bin/python
#
# Created on Aug 25, 2016
# @author: Gaurav Rastogi (grastogi@avinetworks.com)
# Eric Anderson (eanderson@avinetworks.com)
# module_check: supported
# Avi Version: 17.1.1
#
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the te... | kbrebanov/ansible | lib/ansible/modules/network/avi/avi_cloudconnectoruser.py | Python | gpl-3.0 | 3,688 | [
"VisIt"
] | d9b5c8c8d302aef44521ddd440c53438a3db85015beb6bc8f24f1b4cdd4503e4 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# ---------------------------------------------------------------------
# Copyright (c) 2012 Michael Hull.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions
# are m... | mikehulluk/morphforge | src/morphforgecontrib/simulation/channels/hh_style/core/mmleak.py | Python | bsd-2-clause | 2,818 | [
"Elk"
] | a2a4dc44218f7da3e6cdddba7604308490b02653f1547cc97785d794d5e9b895 |
"""
Student Views
"""
import datetime
import logging
import uuid
import json
import warnings
from collections import defaultdict
from urlparse import urljoin, urlsplit, parse_qs, urlunsplit
from django.views.generic import TemplateView
from pytz import UTC
from requests import HTTPError
from ipware.ip import get_ip
im... | prarthitm/edxplatform | common/djangoapps/student/views.py | Python | agpl-3.0 | 109,949 | [
"VisIt"
] | 61bea4b4bcaa5b95e4c48a18b60ea253bd2a577b9a170790749b0468c8801ca1 |
#!/usr/bin/python
# script for computing overlap signatures from a bowtie output
# Christophe Antoniewski <drosofff@gmail.com>
# Usage signature.py <1:input> <2:format of input> <3:minsize query> <4:maxsize query> <5:minsize target> <6:maxsize target>
# <7:minscope> <8:maxscope> <9:output> <10:bowtie index> <11:pro... | JuPeg/tools-artbio | tools/msp_sr_signature/signature.py | Python | mit | 5,521 | [
"Bowtie"
] | c491b39e2c8d0e282125a843a7d014622c07e1881d275f19e9bf79100e452fd7 |
# synapse.py ---
#
# Filename: synapse.py
# Description:
# Author:
# Maintainer:
# Created: Sat Jun 29 11:32:29 2013 (+0530)
# Version:
# Last-Updated: Thu Oct 2 2014 (+0530)
# By: Upi
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#
#
#
#
# Change log:
#
#
#
#
# This program is ... | dilawar/moose-full | moose-examples/snippets/synapse.py | Python | gpl-2.0 | 2,394 | [
"MOOSE"
] | 479c19272f1fc66ff92e6d7bf031cc7441cf5ed7283013845ccfffdee313b9a5 |
# (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... | majidaldo/ansible | lib/ansible/utils/__init__.py | Python | gpl-3.0 | 60,421 | [
"Galaxy",
"VisIt"
] | 31057f81bf8d49a2ebbf24c594aa8efa4b88e8cbb107afb8c99b8c9b53d51da2 |
#
# Copyright (C) 2013,2014 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any l... | sehrhardt/espresso | samples/python/not-working/globals.py | Python | gpl-3.0 | 19,983 | [
"ESPResSo"
] | e97e7a741d8d927ca8e4ccda85ad6d57a300542ff838f6d2240479facd079076 |
Licence = """
<OWNER> = Shriharsh Tendulkar (McGill)
<YEAR> = 2015
Module to generate simulated data from CHIME. Inserts fake signals as requested.
"""
import numpy as np
from numpy import random
from matplotlib import pyplot as plt
VERBOSE = True
class AmplitudeTimeSeries:
"""
Defines a class of amplitude... | shriharshtendulkar/FRBSignalGeneration | FRBSignalGeneration.py | Python | mit | 11,295 | [
"Gaussian"
] | 37cc6389412b150d99a87d6f1882cc2db4015705aedcfe0b37643408ddeb369d |
# -*- coding: utf-8 -*-
"""
Wrapper class to compensate for vtk5.4 / designer incompability
"""
from vtk.qt4.QVTKRenderWindowInteractor import QVTKRenderWindowInteractor
class QVTKWidget(QVTKRenderWindowInteractor):
"""
Simple Wrapper without own functionality.
"""
pass
| tscholze/ts-py-planet-sim | stable/QVTKWidget.py | Python | mit | 296 | [
"VTK"
] | ac5a3b4fea40cb8d6dcd4be40cc794657a4b3559fdd81f7789c3fe22e4fb48fa |
#!/usr/bin/env python
import sys
import versioneer
from setuptools import find_packages, setup
DISTNAME = 'xarray'
LICENSE = 'Apache'
AUTHOR = 'xarray Developers'
AUTHOR_EMAIL = 'xarray@googlegroups.com'
URL = 'https://github.com/pydata/xarray'
CLASSIFIERS = [
'Development Status :: 4 - Beta',
'License :: OSI... | shoyer/xray | setup.py | Python | apache-2.0 | 4,181 | [
"NetCDF"
] | 26aa761bf9126a9606ea4391c5274f0e8b37896ef3ac14817866229828ecbf7a |
import unittest
from test import support
from itertools import *
import weakref
from decimal import Decimal
from fractions import Fraction
import sys
import operator
import random
import copy
import pickle
from functools import reduce
import sys
import struct
maxsize = support.MAX_Py_ssize_t
minsize = -maxsize-1
def l... | MalloyPower/parsing-python | front-end/testsuite-python-lib/Python-3.5.0/Lib/test/test_itertools.py | Python | mit | 89,323 | [
"GULP"
] | 4d615fa17a855c334ff30f2a9c7137e8184d151307f8f1ccaf581e128e7334e5 |
"""Configuration file for eruption scenario
Scenario Name: Mount Guntur 1840 (Validation scenario)
This scenario was developed in July 2010 to validate AIM/Fall3d-6.2 against observed ash thicknesses from the Guntur 1840 eruption by
Adele Bear-Crozi... | GeoscienceAustralia/PF3D | validation/guntur/guntur1840.py | Python | gpl-3.0 | 3,644 | [
"Gaussian"
] | a5954863bbe0f105c6757d29839d21e051867ae2a4801439233b1e53bec4fd1b |
# ################################################################
#
# Active Particles on Curved Spaces (APCS)
#
# Author: Silke Henkes
#
# ICSMB, Department of Physics
# University of Aberdeen
#
# Author: Rastko Sknepnek
#
# Division of Physics
# School of Engineering, Physics and Math... | sknepneklab/SAMoS | FormerAnalysis/polar_defects_analysis_debug.py | Python | gpl-3.0 | 26,011 | [
"VTK"
] | bc8a9e44812d52fa3102a1c9a579076f20a58791229e17a90a8c614276285a19 |
# Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import math
import torch
from torch.distributions.utils import lazy_property
from torch.nn.functional import pad
from pyro.distributions.util import broadcast_shape
from pyro.ops.tensor_utils import cholesky, matmul, matvecmul, t... | uber/pyro | pyro/ops/gaussian.py | Python | apache-2.0 | 20,053 | [
"Gaussian"
] | 57a537b74d1fdb3a6778a3a53010409705e2b77fd74de282f338c84cd2323bca |
# python3
# Copyright 2021 The Chromium Authors. All rights reserved.
# Use of this source code is governed by a BSD-style license that can be
# found in the LICENSE file.
"""The gen module implements the gen action.
The gen action will generate the dependency graph of from crates rooted in
`third_party/rust/third_par... | chromium/chromium | tools/crates/lib/gen.py | Python | bsd-3-clause | 51,537 | [
"VisIt"
] | 1113eb44363a86a1733b125a4b47533f95b1524805444ed2faef674f958c4772 |
""" DeadCodeElimination remove useless code. """
from pythran.analyses import PureExpressions, UseDefChain
from pythran.openmp import OMPDirective
from pythran.passmanager import Transformation
import pythran.metadata as metadata
import ast
class DeadCodeElimination(Transformation):
"""
Remove useless state... | hainm/pythran | pythran/optimizations/dead_code_elimination.py | Python | bsd-3-clause | 3,556 | [
"VisIt"
] | e927deb60b451bbd9d96662d4e0825b31678d3fab5a82509bb44b25ab85117aa |
# 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... | mkuron/espresso | testsuite/python/pairs.py | Python | gpl-3.0 | 3,983 | [
"ESPResSo"
] | 87b9d31a1f19ce578c58da4796cc7efdb85037dd6da15879549442163d08b356 |
# Licensed under a 3-clause BSD style license - see LICENSE.rst
"""
Bayesian Blocks for Time Series Analysis
========================================
Dynamic programming algorithm for solving a piecewise-constant model for
various datasets. This is based on the algorithm presented in Scargle
et al 2012 [1]_. This cod... | bsipocz/astropy | astropy/stats/bayesian_blocks.py | Python | bsd-3-clause | 18,511 | [
"Gaussian"
] | b39f1fe3914ebc6692cd0efc451826e5f74f0ed0807b1ebe8e0b07eb9066011e |
#!/usr/bin/python3
# encoding=utf-8
#
# Copyright © 2015 Alexandre Detiste <alexandre@detiste.be>
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your... | a-detiste/game-data-packager | tools/babel.py | Python | gpl-2.0 | 9,022 | [
"VisIt"
] | 125d1c51489ed02e19c49799dc3979fadc8b5f9c005dbe24bfb113315be8b2b1 |
# coding=utf-8
# Copyright 2022 The Google Research 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 applicab... | google-research/google-research | mol_dqn/chemgraph/dqn/molecules.py | Python | apache-2.0 | 18,564 | [
"RDKit"
] | 256a3c81cd30517d095f2d1bf1a1b55a0cfabb397cdbd4b5f5a18f4bcd4aa6ef |
# 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 | Testing/SystemTests/tests/analysis/AbinsTest.py | Python | gpl-3.0 | 17,926 | [
"CASTEP",
"CRYSTAL",
"DMol3",
"Gaussian"
] | 11e1cb9f70b4cb57709c3e2da9944c9108490421e82501ef5be94a8ca32eca69 |
# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class Macsio(CMakePackage):
"""A Multi-purpose, Application-Centric, Scalable I/O Proxy Applicat... | iulian787/spack | var/spack/repos/builtin/packages/macsio/package.py | Python | lgpl-2.1 | 4,202 | [
"NetCDF"
] | 0fe75650329fba0d8d8b74a985e365fa9a1da4e7033bbc3ba4ce1d4251d92daf |
# -*- coding: ISO-8859-15 -*-
# =============================================================================
# Copyright (c) 2004, 2006 Sean C. Gillies
# Copyright (c) 2007 STFC <http://www.stfc.ac.uk>
#
# Authors :
# Dominic Lowe <d.lowe@rl.ac.uk>
#
# Contact email: d.lowe@rl.ac.uk
# =======================... | sebastic/QGIS | python/ext-libs/owslib/coverage/wcs100.py | Python | gpl-2.0 | 18,814 | [
"NetCDF"
] | 0b6074f0e620ca1bfe80681af80553f83bda74cf0583ca5c1b6c9665c8ba7acb |
#!/usr/bin/env python
"""
This module provides classes to define substructural components of periodic structures
"""
from __future__ import division
__author__ = "Stephen_Dacek"
__credits__ = 'Lusann Wren Yang'
__copyright__ = "Copyright 2014, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Stephen Dace... | tchen0965/structural_descriptors_repo | substructure.py | Python | mit | 15,936 | [
"pymatgen"
] | 055a64b2625138c2e795b22f51b0ff40ce0b790413f062e780e0de9cd5bd75df |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
This file is part of XBMC Mega Pack Addon.
Copyright (C) 2014 Wolverine (xbmcmegapack@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... | xbmcmegapack/plugin.video.megapack.dev | resources/lib/config.py | Python | gpl-3.0 | 11,926 | [
"VisIt"
] | 5dad7ddb742e78551c71602af2a1352011ea4ac3453bb0a28dc2845c90ac1175 |
"""Likelihood objects for inference within the GLM framework."""
from __future__ import division
import numpy as np
from scipy.stats import bernoulli, binom, poisson, norm, gamma
from scipy.special import gammaln, expit
from .btypes import Parameter, Positive
from .mathfun.special import safesoftplus, softplus
#
... | NICTA/revrand | revrand/likelihoods.py | Python | apache-2.0 | 15,411 | [
"Gaussian"
] | 0838b05b35a1014b067b9fd3f66b4e63c9a16c3e0cc6d4c2b7f4e406bffb381e |
# Written by Lauri Lehtovaara, 2007
"""This module implements time propagators for time-dependent density
functional theory calculations."""
import sys
import numpy as np
from gpaw.utilities.blas import axpy
from gpaw.utilities.blas import dotc
from gpaw.mpi import rank, run
from gpaw.tddft.utils import MultiBlas... | robwarm/gpaw-symm | gpaw/tddft/propagators.py | Python | gpl-3.0 | 64,747 | [
"GPAW"
] | 406add32828d0fa031b88543fc97947dfb4da3b6d473a3612e306802cc75e546 |
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft = python sts = 4 ts = 4 sw = 4 et:
"""Afni preprocessing interfaces
Change directory to provide relative paths for doctests
>>> import os
>>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
>>> datadir = o... | sgiavasis/nipype | nipype/interfaces/afni/preprocess.py | Python | bsd-3-clause | 110,632 | [
"Gaussian"
] | f29cc5202a60b9305715b2af1c4260d0c3ece22e26699d520726ebe8a48e8a9f |
import unittest
class TestDicts(unittest.TestCase):
"Testing dictionary functions"
def test_dict_conversion(self):
ls = [['Yankees', 7], ['Red Sox', 0]]
d = dict(ls)
self.assertEqual(d['Yankees'], 7)
def test_string_to_dict(self):
cypher = ['an', 'bo', 'cp', 'dq']
mapping = dict(cypher)
... | jake-bladt/pysandbox | 001-unittest/test_dicts.py | Python | apache-2.0 | 857 | [
"Brian"
] | ff3aed6d8dbea6c8dd363dfb260a9e20a97caf679866baf21a5ae10c95c84617 |
#!/usr/bin/env python
from __future__ import print_function
import argparse
import subprocess
import sys
import os
import numpy as np
from scipy.io import netcdf
##########################################################################
# FUNCTIONS
###################################################################... | vanessajurtz/lasagne4bio | peptide_MHCII/scripts/seq2bl.py | Python | gpl-3.0 | 7,560 | [
"NetCDF"
] | 48fbf26fa84ab4342ca18398b1f44c745613d9efed90dfdda2a538d94b78a10e |
# coding: utf-8
"""Test mdn.kumascript."""
from __future__ import unicode_literals
from django.utils.six import text_type
from mdn.html import HTMLText
from mdn.kumascript import (
Bug, CSSBox, CSSxRef, CompatAndroid, CompatChrome, CompatGeckoDesktop,
CompatGeckoFxOS, CompatGeckoMobile, CompatIE, CompatNightl... | renoirb/browsercompat | mdn/tests/test_kumascript.py | Python | mpl-2.0 | 39,219 | [
"VisIt"
] | 7245cd1d76a5e6884b9776b7dc6351c8fa043e72e903cd840b6b7cf1011df0a9 |
from simtk.unit import kilocalories_per_mole, kilojoules_per_mole, nanometer, angstrom, picosecond
import numpy
# --- Test OpenMMAmberPotential
from pele.amber.openmm_potential import OpenMMAmberPotential
# create potential for the molecule in coords.pdb
prmtopFname = '../aladipep/coords.prmtop'
inpcrdFname = ... | kjs73/pele | playground/amber/testOpenMM/testOpenMM_in_PELE.py | Python | gpl-3.0 | 2,164 | [
"Amber",
"OpenMM"
] | c6d3efb9b365acb570e33ce321cf608565464028944f0a92bd6f67948fb6c44f |
import numpy as np
DELTA_T_CALENDARS = 4857 # Difference between modern and ancient calendar in years
CURRENT_YEAR = 2019 # Current year according to the modern calendar
DAYS_PER_YEAR = 365.25 # Assumed number of days per year
N_A = 6.02214076e23 # Avogadro constant in 1/mol
MOLAR_MASS_C14 = 14.003241 # Molar mas... | dsavoiu/kafe2 | examples/007_cost_functions/generate_data_radiocarbon_dating.py | Python | gpl-3.0 | 2,114 | [
"Avogadro"
] | 239893e71c3304b14ff428febd2dff861bba580a02ff5dba0b27d1043b4c380b |
from __future__ import absolute_import
from __future__ import print_function
from __future__ import division
import time
import os
import numpy as np
import scipy
import scipy.misc
from skopt import gp_minimize
from skopt.space import Categorical
def expansion_number_to_string(expansion):
if expansion == 0:
... | AlbertoEsc/cuicuilco | hyperparameter_search.py | Python | apache-2.0 | 26,403 | [
"Gaussian"
] | a60b7ca041539d0c2d508c434d307486818beecea133b29ee1b17ba3100b2f72 |
#!/usr/bin/env python
"""
Example script showing how to use lmatools to sort LMA ASCII data into flashes
and how to create gridded imagery from those flashes.
The block of code at the bottom shows how to call sorting and gridding functions.
The params dictionary controls the flash sorting parameters.
USAGE:
python f... | deeplycloudy/lmatools | examples/flash_sort_and_grid.py | Python | bsd-2-clause | 8,620 | [
"NetCDF"
] | c2a31ba5c5625205be4d0a5349a3ce081f9d6aba887d52ebb3c4ee03768543b0 |
# Orca
#
# Copyright 2007-2008 Sun Microsystems Inc.
#
# 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 2.1 of the License, or (at your option) any later version.
#
# This... | Alberto-Beralix/Beralix | i386-squashfs-root/usr/share/pyshared/orca/scripts/apps/gnome-system-monitor/__init__.py | Python | gpl-3.0 | 857 | [
"ORCA"
] | 0ffdea8c0e57ccab3c38d7d3e12f5ada551f1a2e366dd0195ea352d955280574 |
#!/usr/bin/env python
"""
Easy Install
------------
A tool for doing automatic download/extract/build of distutils-based Python
packages. For detailed documentation, see the accompanying EasyInstall.txt
file, or visit the `EasyInstall home page`__.
__ https://setuptools.readthedocs.io/en/latest/easy_install.html
""... | aguestuser/social-network-analysis-sandbox | lib/python3.5/site-packages/setuptools/command/easy_install.py | Python | gpl-3.0 | 88,319 | [
"VisIt"
] | 2a42a83faa055230c7c626373e25d7076d786cd9e2969b94fdc57141853c85e9 |
# $Id$
#
# Copyright (C) 2003-2006 Rational Discovery LLC
#
# @@ All Rights Reserved @@
# This file is part of the RDKit.
# The contents are covered by the terms of the BSD license
# which is included in the file license.txt, found at the root
# of the RDKit source tree.
#
import random
import unittest
from rdki... | rvianello/rdkit | rdkit/DataStructs/UnitTestTopNContainer.py | Python | bsd-3-clause | 2,548 | [
"RDKit"
] | 20773476a8da289af832edfd0f45322869683b63f39d05c7780f3825b25eede1 |
# ==================================================================================================
# Copyright 2011 Twitter, Inc.
# --------------------------------------------------------------------------------------------------
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use thi... | foursquare/commons-old | src/python/twitter/pants/python/python_chroot.py | Python | apache-2.0 | 8,008 | [
"Brian"
] | 2bf3c48c62278fe989ef6d70ff5e5976ac9136cf21c81086ac65f483cb05f407 |
"""
Implements a class for performing Basis Adaptation using the Active Subspace method.
Author: Panos Tsilifis
Date: 2/7/2017
"""
__all__ = ['ActiveSubspaceAdaptation', 'GaussianAdaptation', 'QuadraticAdaptation']
import numpy as np
import scipy.stats as st
from . import PolyBasis
from . import MonicPoly
from . i... | tsilifis/chaos_basispy | chaos_basispy/_AS_adaptation.py | Python | gpl-3.0 | 5,655 | [
"Gaussian"
] | e46dc81d5e3256fb0a51e8119632affda4d697d9ceae2ad4c2849babf0011471 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This module implements symmetry-related structure forms.
"""
from typing import List, Sequence
import numpy as np
from tabulate import tabulate
from pymatgen.core.structure import PeriodicSite, Structure... | richardtran415/pymatgen | pymatgen/symmetry/structure.py | Python | mit | 5,212 | [
"pymatgen"
] | a9b1e2bbb8f845d5817eb32168a3b71ac22da06e6890dd671846f10c47e48f74 |
""" StateMachine unit tests
"""
import diracmock
SUT_PATH = 'DIRAC.ResourceStatusSystem.PolicySystem.StateMachine'
# Tests ........................................................................
class State_test( diracmock.DIRAC_TestCase ):
""" State_test
"""
sutPath = SUT_PATH
def test_instant... | Sbalbp/DIRAC | ResourceStatusSystem/PolicySystem/test/test_StateMachine.py | Python | gpl-3.0 | 9,452 | [
"DIRAC"
] | 266d82e481a22221b19cd05f9a964ac5d52c21314ebb6112e6efd215d51a81ad |
from .lpi_filter import inverse, wiener, LPIFilter2D
from ._gaussian import gaussian
from .edges import (sobel, sobel_h, sobel_v,
scharr, scharr_h, scharr_v,
prewitt, prewitt_h, prewitt_v,
roberts, roberts_pos_diag, roberts_neg_diag,
laplac... | paalge/scikit-image | skimage/filters/__init__.py | Python | bsd-3-clause | 2,112 | [
"Gaussian"
] | d6f52e811e049c9af5f03d832252cacb4c9a9d7d685022ed7de2d44a67739a92 |
#! /usr/bin/python3
import SnnBase
import Stdp
import DopamineStdp
import random
class NoisySpikingNeuron(SnnBase.SpikingNeuron):
def __init__(self, *args, **kwargs):
super().__init__(*args, **kwargs)
self.gross_error = 0.0
self._spike_mode = random.choice([True, False])
def set_g... | boldingd/BadSnn | rule_scratch_2.py | Python | bsd-3-clause | 20,431 | [
"NEURON"
] | 1e86ba8a127d2a31c8c5a2c2fd275c46894a8f8fcc3109be74296b3715d777aa |
# pylint: disable=C0111
# pylint: disable=W0621
from lettuce import world
from django.contrib.auth.models import User, Group
from student.models import CourseEnrollment
from xmodule.modulestore.django import editable_modulestore
from xmodule.contentstore.django import contentstore
@world.absorb
def create_user(uname... | TsinghuaX/edx-platform | common/djangoapps/terrain/course_helpers.py | Python | agpl-3.0 | 2,346 | [
"VisIt"
] | 9f3ca7b575da68b4a07426511a1c2c9f8bec30daad91e1005fc2dda388492d34 |
# This file is meant primarily for people who want to see an example
# of how to use part of the OpenBabel API, with a secondary use as a
# set of quick unit tests to make sure there's no strange but obvious
# problem with your OpenBabel setup.
# Regression tests, coverage tests, stress tests, performance tests,
# etc... | dkoes/openbabel | scripts/python/examples/dalke_test.py | Python | gpl-2.0 | 45,308 | [
"Open Babel"
] | e88f659059e2c368ad466bda76b5bcb090ce4ea213564a41e5d5f0ddf5050db4 |
#!/usr/bin/env python
# filter_contigs.py
# June 2012 Matthew MacManes (macmanes@gmail.com)
#
# This wrapper is free software: you can redistribute it and/or modify
#
import sys
import subprocess
import optparse
import shutil
import os
from datetime import datetime, date, time
from Bio import SeqIO
print ... | macmanes/trinityrnaseq | util/eXpress_util/filter_contigs.py | Python | bsd-3-clause | 3,548 | [
"Biopython"
] | 2e89f0986db798fe342cea1d38004327ff40d0814c01549ae7737a3d9d831971 |
"""Infrastructure for RNA-seq supporting files.
"""
import os
import subprocess
from cloudbio.custom import shared
def finalize(genomes, data_filedir):
"""Provide symlinks back to reference genomes so tophat avoids generating FASTA genomes.
"""
genome_dir = os.path.join(data_filedir, "genomes")
for (o... | chapmanb/cloudbiolinux | cloudbio/biodata/rnaseq.py | Python | mit | 1,394 | [
"Bowtie"
] | c7b66c7633f8a75dde7f083dfd951292e8d3b0246e3461b057c2ec4ac384f1be |
#! /usr/bin/env python
#TODO: remove all implicit type casting
#
#TODO: fix the gt/lt operators
# isinstance((A > [1,2,3]) == [True,False,True],float)
# isinstance((A > [1,2,3]).any(),float)
# isinstance((A > [1,2,3]).all(),float)
#
#TODO: better interoperability with scipy.stats
#TODO:... | MarkDaoust/mvn | mvn/__init__.py | Python | bsd-2-clause | 91,756 | [
"Gaussian",
"Mayavi"
] | ce095ad4f7f989cb768424695ff1da14d5e90c885e5bb84aac67aad5663ea868 |
#!/usr/bin/env python
'''Preprocessing scripts
'''
import abc
import random
import numpy as np
from skimage import exposure, feature
import skimage.filters
class ImagePreprocessor(object):
__metaclass__ = abc.ABCMeta
def __init__(self):
pass
@abc.abstractmethod
def _process_one_image(self, ... | wclark3/machine-learning | final-project/code/preprocess.py | Python | mit | 8,004 | [
"Gaussian"
] | e1a500e52f8d3e36524389622c8b3ecbc039270aed27162eaa3030857f659443 |
from . import _whitenoise
import numpy
def generate(complex, start, Nmesh, seed, unitary):
"""
unitary : bool
True for a unitary gaussian field (amplitude is fixed to 1)
False for a true gaussian field
"""
_start = numpy.empty(complex.ndim, dtype='intp')
_Nmesh = numpy.e... | nickhand/pypm | pmesh/whitenoise.py | Python | gpl-3.0 | 1,364 | [
"Gaussian"
] | 49ae3a2acd6b0ef1011ea39ffaa65bdaf3301450629a43a1f9f44bced646f23c |
#
# File: geometry.py
# Author: Bo-Xiao Zheng <boxiao@princeton.edu>
#
import numpy as np
import numpy.linalg as la
import itertools as it
class FHamHubbard(object):
def __init__(self, U, t = 1.):
self.U = U
self.t = t
self.transinv = True
def build_h0(self, lattice):
bc = lat... | zhengbx/BBQ | ham.py | Python | gpl-3.0 | 5,088 | [
"CRYSTAL"
] | 6bf9d2dc754d4309347f41891203989a46868c8a852c24f868cd296146f7d228 |
"""
General Numerical Solver for the 1D Time-Dependent Schrodinger's equation.
author: Jake Vanderplas
email: vanderplas@astro.washington.edu
website: http://jakevdp.github.com
license: BSD
Please feel free to use and modify this, but keep the above information. Thanks!
"""
import numpy as np
from matplotlib import p... | benvchurch/project-eva | Schrodinger_Solver/schrodinger.py | Python | unlicense | 9,289 | [
"Gaussian"
] | e53718da1b6abf1c342b34292752ba8a0aecabf94a23987260b7e4aa7e477abd |
###############################################################################
# Copyright 2013-2014 The University of Texas at Austin #
# #
# Licensed under the Apache License, Version 2.0 (the "License"); #... | ericblau/ipf-xsede | ipf/glue2/modules.py | Python | apache-2.0 | 16,193 | [
"VisIt"
] | c4369bad4c6978306a2f05cf7c656c091f17f773a817433e2b8d659b0c8c9d8f |
#!/usr/bin/env python
#
# Electrum - Lightweight Bitcoin Client
# Copyright (C) 2015 Thomas Voegtlin
#
# 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 y... | akshayaurora/electrum | plugins/trustedcoin/qt.py | Python | gpl-3.0 | 11,013 | [
"VisIt"
] | 69adc5057231d81e9863b68f991a592e07bd08670504ac2881c982c2199931c3 |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/test/test_proxy.py | Python | gpl-2.0 | 6,450 | [
"VisIt"
] | c4c7ecd140e7b58bfaed4035fef468f0da072c0b76b39442133125245702179b |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
class Migration(migrations.Migration):
dependencies = [
('visit', '0035_auto_20150722_2007'),
]
operations = [
migrations.AlterField(
model_name='visit',
name... | koebbe/homeworks | visit/migrations/0036_auto_20150722_2033.py | Python | mit | 615 | [
"VisIt"
] | 2d4ce086ce13c29868c2b4a368eac29a3c14474a340245dc7be0ebc56be0589e |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2007 Zsolt Foldvari
# Copyright (C) 2008 Brian G. Matherly
# Copyright (C) 2013 Vassilii Khachaturov
#
# 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 F... | jralls/gramps | gramps/plugins/docgen/cairodoc.py | Python | gpl-2.0 | 11,818 | [
"Brian"
] | 5c7066b7633f1a646fe8550bdba21208369856f7d2b1727436798d2fc161ecf8 |
# -*- coding: utf-8 -*-
# Copyright 2013 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 require... | ychen820/microblog | y/google-cloud-sdk/platform/gsutil/gslib/addlhelp/creds.py | Python | bsd-3-clause | 8,063 | [
"VisIt"
] | eb82153d2d72856272c9b847f4a7208d5bd92987387c0bfb6ba03d1ebd7b8f12 |
# 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 | seal/seqal/mapper.py | Python | gpl-3.0 | 27,924 | [
"BWA"
] | ba63828e3fd3ac102692a6ea2adbd9c376dc543186dcf2c82d03489296a74a78 |
from __future__ import unicode_literals
from django.conf import settings
from django.contrib.auth.models import User
from django.core import mail
from django.template import TemplateSyntaxError
from django.utils.six.moves.urllib.request import urlopen
from djblets.siteconfig.models import SiteConfiguration
from djblet... | custode/reviewboard | reviewboard/notifications/tests.py | Python | mit | 43,976 | [
"VisIt"
] | 815a61ad0605abb8b3b6093c6a2855eb14fbac85d137c8a43ed67559aec4332a |
# Author: Samuel Genheden samuel.genheden@gmail.com
"""
Program to rename atoms and residue
Examples
--------
pdb_rename.py mystruct.pdb -atoms POPC=names_popc.txt TIP3P=names_wat.txt -from Charmm -to Berger -residues TIP3P=SOL
"""
import argparse
import os
import sys
import numpy as np
from sgenlib import pdb
... | SGenheden/Scripts | Pdb/pdb_rename.py | Python | mit | 1,978 | [
"CHARMM"
] | 4aa467828fa91c026d621dc9f03416d6578735869a2d7b464ae7746cb275d389 |
"""
You run a successful software consulting business, and you've just gotten a visit
from Earl, who runs the local library. He's looking for software that will help
him manage his very peculiar checkout process.
"Organizing books is hard," says Earl. "I gave up on it years ago. Nowadays when
you come into the libr... | efulet/library-sample | library/library.py | Python | mit | 3,930 | [
"VisIt"
] | 009d1aebee0734291153ca8dec66aaac64d32a50c4c550ffebd90296f3c06254 |
import os.path
import json
import pytz
from collections import defaultdict
from datetime import datetime
from dateutil import parser
class Data:
"""
Class to describe event data
"""
# Customer Events Master data
customer_master_dict = defaultdict(dict)
# Orders Master Data
order_master_... | shashanklmur/code_ch | src/code_challenge.py | Python | apache-2.0 | 5,368 | [
"VisIt"
] | 8d9d98d2c9ccbb0dd3b59f19a4ced9a0ea085ac8ac044d8dfd804e1723554911 |
# -*- coding: utf-8 -*-
"""
State Space Model
Author: Chad Fulton
License: Simplified-BSD
"""
from statsmodels.compat.pandas import is_int_index
import contextlib
import warnings
import datetime as dt
from types import SimpleNamespace
import numpy as np
import pandas as pd
from scipy.stats import norm
from statsmod... | statsmodels/statsmodels | statsmodels/tsa/statespace/mlemodel.py | Python | bsd-3-clause | 212,431 | [
"Gaussian"
] | b0dbb0882cb4a56d5861a8dc8bb567f5ace9fd91ea500de97372d3a69e3e066a |
import os
import posixpath
import six
import stat
import re
import uuid
import fnmatch
from fabric.state import output, connections, env, win32
from fabric.utils import warn
from fabric.context_managers import settings
# TODO: use self.sftp.listdir_iter on Paramiko 1.15+
def _format_local(local_path, local_is_path... | ploxiln/fabric | fabric/sftp.py | Python | bsd-2-clause | 12,835 | [
"VisIt"
] | 45914551b134df15ce834548a3152cb1be8c705928c71c91f90ca475f641072f |
''' CEAvailabilityCommand module
'''
# FIXME: NOT Usable ATM
# missing doNew, doCache, doMaster
__RCSID__ = '$Id$'
from DIRAC import S_OK, S_ERROR
from DIRAC.ResourceStatusSystem.Command.Command import Command
from DIRAC.Interfaces.API.DiracAdmin import DiracAdmin
from DIRAC.ConfigurationSystem.Client.Helpers.Regist... | andresailer/DIRAC | ResourceStatusSystem/Command/CEAvailabilityCommand.py | Python | gpl-3.0 | 2,607 | [
"DIRAC"
] | a55b4a1a8846b7df12e57671f5005ec823e7f4c39bb35085878368d0c8353420 |
#
# 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... | mxm/incubator-beam | sdks/python/apache_beam/examples/snippets/snippets.py | Python | apache-2.0 | 47,110 | [
"VisIt"
] | 408c73d3040b726edb0529f222850b73f2d8008d8a5f04bee21b3885906de506 |
# This code is part of Ansible, but is an independent component.
# This particular file snippet, and this file snippet only, is BSD licensed.
# Modules you write using this snippet, which is embedded dynamically by Ansible
# still belong to the author of the module, and may assign their own license
# to the complete wo... | bjolivot/ansible | lib/ansible/module_utils/basic.py | Python | gpl-3.0 | 100,248 | [
"VisIt"
] | 27c37f7ce461be489f1a6debb5cc6e8a857a92c39e9f978a79a290194a3aee53 |
from django.db import models
class Organization(models.Model):
owner = models.ForeignKey('auth.User',related_name="organizations")
name = models.CharField(max_length=128)
created = models.DateTimeField(auto_now_add=True)
class Household(models.Model):
organization = models.ForeignKey(Organization,related_name="ho... | ryanrborn/lds-leader-tool-suite-backend | llts/models.py | Python | mit | 2,263 | [
"VisIt"
] | 1631e24bba161bbaa231cff6dfe82d1e889973b844ee43f3dab1879e912a54ac |
# $Id$
#
# Copyright (c) 2007, 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 above... | bp-kelley/rdkit | Projects/DbCLI/CreateDb.py | Python | bsd-3-clause | 20,726 | [
"RDKit"
] | d7c89ff43a24be4e252a7ad01387c0ae0f0d042511e1b33d54ace351bdf9a933 |
# -*- coding: utf-8 -*-
"""
Created ATP profile input data based on rescaling CDF output.
"""
import os
import vtk
inputFile = ''
inputSurfaceFile = ''
outputFile = ''
outputSurfaceFile = ''
outMin = 0.0
outMax = 1.0
def rescale(val, inMin, inMax):
return (val - inMin) * (outMax - outMin) / (inMax - inMin) + ou... | BlueFern/DBiharMesher | util/RescaleATPToRange.py | Python | gpl-2.0 | 2,022 | [
"VTK"
] | 07a3300834dc52e4c0c13aa44ceadb97325cc1ccc6458ae66e2efe14f4dd8ee4 |
# -*- 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-game-servers | tests/unit/gapic/gaming_v1/test_game_server_deployments_service.py | Python | apache-2.0 | 140,577 | [
"Octopus"
] | 186fb9fa8b84ba5cd014351d8af3329807746f0f50021bf806282d829b7db5dc |
import copy
import matplotlib.pyplot as plt
import matplotlib.gridspec as gs
import numpy as np
from scipy.stats import norm
from pyterpol.synthetic.auxiliary import read_text_file
def get_walker(db, nchain, nwalker, niter):
"""
Retrieves a walker from the chain.
:param db:
:param nchain:
:param n... | chrysante87/pyterpol | plotting/plotting.py | Python | gpl-2.0 | 9,041 | [
"Gaussian"
] | 095023b1318d4767816aa8f5afc91bc5e9de11bb8c68c600055938a9b160b727 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2017 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
#... | rmcgibbo/psi4public | psi4/driver/p4util/optproc.py | Python | lgpl-3.0 | 4,714 | [
"Psi4"
] | ab49e615733f5ce8457777d01fb8323681d1d2eaac47bc0418acd05f55d61c42 |
import numpy as np
import MDP
class RL:
def __init__(self,mdp,sampleReward):
'''Constructor for the RL class
Inputs:
mdp -- Markov decision process (T, R, discount)
sampleReward -- Function to sample rewards (e.g., bernoulli, Gaussian).
This function takes one argument: the... | li-ch/mind | scripts/RL.py | Python | mit | 5,183 | [
"Gaussian"
] | b2e80a504062d5297755077c5fbecb4386c8b5a6057a05946fa981f7862635a9 |
"""Test transient simulation functions."""
from pytest import raises
from neurodsp.sim.transients import *
###################################################################################################
###################################################################################################
N_SECONDS... | srcole/neurodsp | neurodsp/tests/test_sim_transients.py | Python | mit | 1,472 | [
"Gaussian"
] | 459b23f4fc4e56b7c8432bec8356e554e74c7243d73bb811900dd1dfa7db2227 |
# $HeadURL$
"""
The Grid module contains several utilities for grid operations
"""
__RCSID__ = "$Id$"
import os
import types
import re
from DIRAC.Core.Utilities.Os import sourceEnv
from DIRAC.FrameworkSystem.Client.ProxyManagerClient import gProxyManager
from DIRAC.Core.Security.ProxyInfo import g... | Sbalbp/DIRAC | Core/Utilities/Grid.py | Python | gpl-3.0 | 15,413 | [
"DIRAC"
] | cd396b037603871b4926ba5d2a41a26dd6a18058a150ac31172433dce2b7fcfa |
import unittest
import pysal
import numpy as np
from scipy import sparse
#from pysal.spreg import error_sp_het as HET
from functools import partial
from pysal.contrib.handler import Model
GM_Error_Het = partial(Model, mtype='GM_Error_Het')
GM_Endog_Error_Het = partial(Model, mtype='GM_Endog_Error_Het')
GM_Combo_Het = ... | schmidtc/pysal | pysal/contrib/handler/tests/test_error_spet_sparse.py | Python | bsd-3-clause | 20,565 | [
"COLUMBUS"
] | cbe5df99196ddcafbe965bf78b4d0dcc5af1aa98250b7b30c653a290a0c61bf3 |
# -*- coding: utf-8 -*-
"""\
Visualizing Parameters in a Modern Neural Network
=================================================
"""
from __future__ import (absolute_import, unicode_literals, print_function)
print(__doc__)
__author__ = 'Alex J. Champandard'
import sys
import time
import logging
import argparse
import... | aigamedev/scikit-neuralnetwork | examples/plot_mlp.py | Python | bsd-3-clause | 5,525 | [
"Gaussian"
] | ccab9629165c6e55616e632bc71b9a3f087fa6e765b49ad1c3d1bc615ac6dc67 |
# mencoder "mf://mpg_288x288x24_lam15_t273_a0353140_0000_rv.dat_%d.png" -mf fps=20 -o anim.avi -ovc lavc -lavcopts vcodec=msmpeg4v2:vbitrate=500
import numpy
import sys
from mmdlab.datareader import readfile_track_fast
from mmdlab.utils import make_mlab_scalar_field
from mmdlab.utils import show_scalar_planes
from mmd... | detorto/mdvis | src/part_nterp_reg.py | Python | mit | 3,986 | [
"Mayavi"
] | 73e62f15b7188ecd741f713c55a42175101effb9738459c5e61460cb0db1208a |
# -*- coding: utf-8 -*-
"""
Created on Thu Dec 5 12:30:26 2013
@author: Daniel Struck
create blast results for the COMET <> BLAST LANL comparison:
blastn -num_threads 12 -db training_subtype_03.fasta -query ../lanl_comparison/dataset/2013-08-30_pol_lanl.fasta -num_descriptions 1 -num_alignments 0 > blast_lanl_pol.tx... | dstruck/comet-paper-scripts | compare_blast_comet/import_blast_results_into_database.py | Python | gpl-2.0 | 995 | [
"BLAST"
] | 3914256620637350bc09bf90071b8310631182e1a9c2305d047639616e0900ff |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# --- BEGIN_HEADER ---
#
# aux - [insert a few words of module description on this line]
# Copyright (C) 2003-2011 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... | heromod/migrid | mig/grsfs-fuse/fs/core/specialized/aux.py | Python | gpl-2.0 | 5,503 | [
"Brian"
] | 658b347bef68f7828fb8f90d258fd349601e867d106a1d02cab2b1ea1c4a1415 |
########################################################################
# $HeadURL $
# File: PhysicalRemoval.py
# Author: Krzysztof.Ciba@NOSPAMgmail.com
# Date: 2013/04/02 11:56:10
########################################################################
""" :mod: PhysicalRemoval
=====================
.. modu... | andresailer/DIRAC | DataManagementSystem/Agent/RequestOperations/PhysicalRemoval.py | Python | gpl-3.0 | 6,627 | [
"DIRAC"
] | f1688830e1825b55f32da5929b54b9f17b990e8be677d6b0ab6b8fcca1a63097 |
# Copyright 2017 Andrey Sobolev, Tilde Materials Informatics (Berlin)
# This file is a part of quantum_esperanto project. The project is licensed under the MIT license.
# See the LICENSE file in the project root for license terms.
"""
A test suite for VASP parser. Tests take every xml file in tests/xml and check if p... | tilde-lab/DFTXMLParser | tests/test_vasp_parser.py | Python | mit | 2,460 | [
"VASP"
] | dbb792694d4de824c04535c6fc59f10027251d9f18108c70094274f32305f964 |
# Copyright 2020 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
#
# https://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, ... | google/objax | objax/privacy/dpsgd/privacyaccountant.py | Python | apache-2.0 | 22,737 | [
"Gaussian"
] | 9923db950959041c7c18d9f8b355a48d95f39b2d977b0c06fd2389bd938d90f3 |
# This component assembles an analysis recipe for the annual adaptive comfort component
#
# Honeybee: A Plugin for Environmental Analysis (GPL) started by Mostapha Sadeghipour Roudsari
#
# This file is part of Honeybee.
#
# Copyright (c) 2013-2015, Chris Mackey <Chris@MackeyArchitecture.com>
# Honeybee is free softw... | samuto/Honeybee | src/Honeybee_Outdoor Comfort Analysis Recipe.py | Python | gpl-3.0 | 40,213 | [
"EPW"
] | 8f451c6211f29dd943d02da45124237876de69f8ed6c9e23529ece97f2be98b7 |
"""
====================
Voigt Profile Fitter
====================
Module API
^^^^^^^^^^
"""
from . import model
import numpy as np
from ...spectrum.moments import moments
import types
try:
import scipy.special
scipyOK = True
except ImportError:
scipyOK = False
def voigt(xarr, amp, xcen, sigma, gamma, no... | jpinedaf/pyspeckit | pyspeckit/spectrum/models/inherited_voigtfitter.py | Python | mit | 3,902 | [
"Gaussian"
] | 6c7d5b97f7f0cac9847eeb4a74800bb12d3aa7fd65b5dfb3899b95647932ed84 |
#
# @BEGIN LICENSE
#
# Psi4: an open-source quantum chemistry software package
#
# Copyright (c) 2007-2019 The Psi4 Developers.
#
# The copyrights for code used from other parties are included in
# the corresponding files.
#
# This file is part of Psi4.
#
# Psi4 is free software; you can redistribute it and/or modify
#... | CDSherrill/psi4 | psi4/driver/p4util/inpsight.py | Python | lgpl-3.0 | 23,185 | [
"Jmol",
"Psi4"
] | f1fd5ec4513f30da27b197c3b2e5a749726e690d924dcdb7939828e1e769024f |
"""
# Copyright (C) 2007 Nathan Ramella (nar@remix.net)
#
# 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 2.1 of the License, or (at your option) any later version.
#
# T... | shouldmakemusic/yaas | LiveOSC/OSCClient.py | Python | gpl-2.0 | 6,446 | [
"VisIt"
] | 9afbc60c8a0d00940e7fc3bc3490735ebdc523117a076ccb6cd44daecee54172 |
# ----------------------------------------------------------------------------
# Copyright (c) 2013--, scikit-bio development team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# --------------------------------------------... | kdmurray91/scikit-bio | skbio/sequence/tests/test_protein.py | Python | bsd-3-clause | 4,851 | [
"scikit-bio"
] | c95c955ea28159b876176437c0f441a08e94807f0504ed593ee109a62afc3e49 |
"""
I'm modifying the halotools tpcf code to add a few more efficincies.
One directly returns the correlation functions from subregions, so I can compute arbitary jackknifes more efficiently
Another is to add a flag for do_auto1 and do_auto2. Sometimes, you wanna compute xi_gg and xi_gm but not xi_mm!
"""
from __fut... | mclaughlin6464/pearce | pearce/mocks/tpcfSubregions.py | Python | mit | 21,979 | [
"Galaxy"
] | 1ac7cec3c54c72137a033ab698029f30a8252106ff1d63c673cf4fec01278e6d |
import vtk
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName("")
#Combine the two data sets
appendFilter = vrk.vtkAppendFilter()
appendFilter.AddInputConnection(reader.GetOutputPort())
appendFilter.Update()
unstructuredGrid = vtk.vtkUnstructuredGrid()
unstructuredGrid.ShallowCopy(appendFilter.GetOutput())
#Writ... | kayarre/Tools | vtk/surface2grid.py | Python | bsd-2-clause | 484 | [
"VTK"
] | 659b98e4e2f9515ec74d51b6b590cbaff169b13e07036772cf550ffff91e5ade |
#!/usr/bin/env python
# Copyright 2017 Calico 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
# https://www.apache.org/licenses/LICENSE-2.0
# Unless required by applicable law or agr... | calico/basenji | bin/akita_data.py | Python | apache-2.0 | 18,918 | [
"Gaussian"
] | 8c146ffcfba92deabc6eb6fc2feeededd4800c86b354e1dcc4cf94ab88e78e46 |
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