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##############################################################################
# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | skosukhin/spack | var/spack/repos/builtin/packages/r-biobase/package.py | Python | lgpl-2.1 | 1,759 | [
"Bioconductor"
] | 44e08c0949659b4f42c6bb23849590ae546f6631352baa1c3919b34bbd234737 |
# # #
# Downscale CRU Historical TS3.x data to a pre-processed climatology
# extent, resolution, reference system
#
# Author: Michael Lindgren (malindgren@alaska.edu)
# # #
# import some modules
import rasterio, xray, os
import numpy as np
import pandas as pd
import numpy as np
class DownscalingUtils( object ):
def... | ua-snap/downscale | snap_scripts/old_scripts/tem_iem_older_scripts_april2018/tem_inputs_iem/old_code/cru_ts_downscaling_class_d.py | Python | mit | 20,625 | [
"NetCDF"
] | c2f78f33bd5c50acd47e420c7c1487f21f129fc6a9acfb4f8b5ef59309eb6556 |
#
# Copyright (C) 2002-2006 greg Landrum and 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.
#
""" utility functionality for ... | greglandrum/rdkit | rdkit/Chem/Pharm2D/Utils.py | Python | bsd-3-clause | 13,122 | [
"RDKit"
] | 4480f9a8b109a34b7d32d1feb89c85d61710bea841f57ca8aad308a39d5ace5f |
# $Id$
#
# Copyright (C) 2000-2006 greg Landrum and 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.
#
""" defines class _Db... | jandom/rdkit | rdkit/Dbase/DbConnection.py | Python | bsd-3-clause | 8,759 | [
"RDKit"
] | 6c447b1c2b40da882f22e80684842c7b80dfb185ee43ba8efbfc7b1704828689 |
'''
Created on Dec 16, 2009
@author: Arnaud Chassagne
'''
try:
import simplejson as json
except ImportError:
import json
from octopus.core.communication.http import Http404, Http400, HttpConflict
from octopus.core.framework import queue
from octopus.dispatcher.model.pool import PoolShare, PoolShareCreationExc... | mikrosimage/OpenRenderManagement | src/octopus/dispatcher/webservice/poolshares.py | Python | bsd-3-clause | 3,717 | [
"Octopus"
] | c6007dbd4952c3df64a935d5cf8585f2b47c72b00ee2fcc4081bcc92c8c28bd1 |
# Copyright 2022, The TensorFlow 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 t... | tensorflow/privacy | tensorflow_privacy/privacy/privacy_tests/membership_inference_attack/advanced_mia.py | Python | apache-2.0 | 11,188 | [
"Gaussian"
] | eae51fc27562e1fff573b26aa191e5b5376247847ba936d2736207441c555126 |
#!/usr/bin/python
import sys
import smbus
import time
bus = smbus.SMBus(1)
MCP79410address = 0x6f # SRAM board address
MCP79410EEPROMaddress = 0x57 # EEPROM address
EEPROM_WRITE = 0xae # DEVICE ADDR for EEPROM (writes)
EEPROM_READ = 0xaf # DEVICE ADDR for EEPROM (reads)
RTCC_WRITE = 0xde... | swishpi/swishPi-pHAT | Drivers/RealTimeClockCalendar/MCP79410RTCC.py | Python | gpl-3.0 | 21,488 | [
"CRYSTAL"
] | 02ca3ab6ee2821f5c3e20f085f9836ff66435992903159af03cb5a7f17c22ac9 |
# Orca
#
# Copyright 2005-2008 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/debug.py | Python | gpl-3.0 | 13,614 | [
"ORCA"
] | 2cf3f83b6eef5a4da9b98de3aac2ae95ba2b91ba4f521ebe9ac7dc4b98860d5d |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2020, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
"""
Basis Function Manipulation
################################
Functions for managing and manipulating basis set data.
Many of the ordering schemes used in computational codes can ... | exa-analytics/atomic | exatomic/algorithms/basis.py | Python | apache-2.0 | 23,596 | [
"Gaussian",
"MOLCAS",
"NWChem"
] | 0f4151fc4965752e22ca71b662c06e709eb549cfba15bed7dcc47aa9435531e7 |
# -*- coding: utf-8 -*-
#
# Instant Press. Instant sites. CMS developed in Web2py Framework
# Site: http://www.instant2press.com
#
# Copyright (c) 2010 Mulone, Pablo Martín
#
# License Code: GPL, General Public License v. 2.0
# License Content: Creative Commons Attribution 3.0
#
# Also visit: www.web2py.com
# ... | aidan-fitz/instant-press | modules/siteinfo.py | Python | gpl-2.0 | 19,732 | [
"VisIt"
] | 7b9e8c377ecae1926559590ce54a490da546f9ccfacc26f833f8964c74609f78 |
# Copyright 2009-2014 Eucalyptus Systems, Inc.
#
# 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; version 3 of the License.
#
# This program is distributed in the hope that it will be useful,
# b... | eucalyptus/euca-python-lib | eucalib/ssl.py | Python | bsd-2-clause | 1,433 | [
"VisIt"
] | 27aca0dcdc9a2eb164020f56be37a104ff27e66f9c0caac9586871f1772d6753 |
%pythoncode{
import dirac
class Dirac:
"""
This is the python class that controls the execution of the
DIRAC algorithm.
The format of the inputs are quite exhaustively described in the
dirac.cpp file.
If you are curious about DIRAC the algorithm please check out
"Identifying Tightly Regulat... | JohnCEarls/AUREA | src/AUREA/learner/src/dirac_supp.py | Python | agpl-3.0 | 15,733 | [
"DIRAC"
] | e36a55d1e7706ed4efb15af79077afe9ef18c82f55fccadf6a34a194b5c2f4bc |
#!/usr/bin/env python3
""" Assignment 3, Exercise 2, INF1340, Fall, 2015. Kanadia
Computer-based immigration office for Kanadia
"""
__author__ = 'Susan Sim'
__email__ = "ses@drsusansim.org"
__copyright__ = "2015 Susan Sim"
__license__ = "MIT License"
import re
import datetime
import json
######################
# ... | rawtoast24/Assignment3 | exercise2.py | Python | mit | 8,899 | [
"VisIt"
] | 1f2eec1f7b566cbe95dd257dfe96aa21deaede52faa2d73a8418d2bd6a3833a5 |
from bellman_ford_algorithm import *
def sssp_spfa(src_vertex, matrix, n):
dist = [inf] * n
dist[src_vertex] = 0
prev = [None] * n
visit = [0] * n
check_vertex_lst = []
# have to be a set, because visit[u]'s condition depends on it
queue = {src_vertex}
while len(queue) > 0:
u... | CheYulin/MSBD5009 | python_playground/shortest_path_fast_algorithm.py | Python | mit | 1,996 | [
"VisIt"
] | b50da32fe0fc8ee30fe120dbc418aa52382018c99b9918a3fc20202478e5f277 |
""" Frontend to MySQL DB AccountingDB
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
__RCSID__ = "$Id$"
import datetime
import time
import threading
import random
from DIRAC.Core.Base.DB import DB
from DIRAC import S_OK, S_ERROR, gConfig
from DIRAC.Fr... | ic-hep/DIRAC | src/DIRAC/AccountingSystem/DB/AccountingDB.py | Python | gpl-3.0 | 71,971 | [
"DIRAC"
] | 563e6d6b42ba692cd8830383b5a03eb1e8715507d4d6e5b2f6a594af947cc7fc |
#!/usr/bin/env python
# Copyright (c) 2006 John Gilman
#
# This software is distributed under the MIT Open Source License.
# <http://www.opensource.org/licenses/mit-license.html>
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation file... | go-bears/Final-Project | weblogo-3.4_rd/test_corebio/test_transform.py | Python | mit | 5,167 | [
"Biopython"
] | 995666a9f38d35aa2731c3efaa2efb8a9f880a1454370747c5f49afb19a0028c |
# Copyright (c) 2021 The Linux Foundation
#
# SPDX-License-Identifier: Apache-2.0
# from https://github.com/spdx/license-list-data/
LICENSE_LIST_VERSION = "3.12"
LICENSES = [
"0BSD",
"389-exception",
"AAL",
"ADSL",
"AFL-1.1",
"AFL-1.2",
"AFL-2.0",
"AFL-2.1",
"AFL-3.0",
"AGPL-1.0",
"AGPL-1.0-onl... | galak/zephyr | scripts/west_commands/zspdx/licenses.py | Python | apache-2.0 | 8,790 | [
"NetCDF"
] | a80d5e5594308da4f83038fe5566504e53f344029adf6a11276c5a5adcb3ccb6 |
#-----------------------------------------------------------------
# pycparser: c_lexer.py
#
# CLexer class: lexer for the C language
#
# Copyright (C) 2008-2011, Eli Bendersky
# License: BSD
#-----------------------------------------------------------------
import re
import sys
import ply.lex
from ply.lex import TOK... | pombredanne/pycparser-1 | pycparser/c_lexer.py | Python | bsd-3-clause | 12,639 | [
"NAMD"
] | 314c3578bbc4cbd7454001a6cff21c9bcdf8ad5a8d1aff18a7e0d5e00ef65620 |
from __future__ import print_function
import os
import Bio
import re
import sys
from Bio import SeqIO
from Bio.Blast import NCBIXML
from Bio import Restriction
from Bio.Restriction import *
from Bio.Alphabet.IUPAC import IUPACAmbiguousDNA
from Bio.Seq import Seq
from Bio.SeqRecord import SeqRecord
from Bio.Blast.Appli... | eatingcrispr/VirtualEating | eating/base.py | Python | apache-2.0 | 17,794 | [
"BLAST",
"CRYSTAL"
] | 61a8ac2f1040cd3a9bef471db37de34a87039534ed5b0844d418ec3fe2b1440d |
# Copyright (c) 2017-2019 Uber Technologies, Inc.
# SPDX-License-Identifier: Apache-2.0
import torch
from torch.distributions import constraints
from pyro.contrib.gp.kernels.kernel import Kernel
from pyro.nn.module import PyroParam
class Constant(Kernel):
r"""
Implementation of Constant kernel:
:ma... | uber/pyro | pyro/contrib/gp/kernels/static.py | Python | apache-2.0 | 1,536 | [
"DIRAC"
] | 5f11bc11b356b0ee684306a43795ab1a6c2d0bf04a69ce08ed49352e93c31f64 |
"""
The following contains a database of small molecules
Data for the G2/97 database are from
Raghavachari, Redfern, and Pople, J. Chem. Phys. Vol. 106, 1063 (1997).
See http://www.cse.anl.gov/Catalysis_and_Energy_Conversion/Computational_Thermochemistry.shtml for the original files.
All numbers are experimental valu... | grhawk/ASE | tools/ase/data/g2_2.py | Python | gpl-2.0 | 65,252 | [
"ASE"
] | 9cb3d8222566be6beb07f5b09af6e7f1ab1e715cdbc2070358008c9a3d86c575 |
"""
SurfacePicker
:Authors:
Berend Klein Haneveld
"""
import math
from Picker import Picker
from ui.Interactor import Interactor
from vtk import vtkVolumePicker
from vtk import vtkActor
from vtk import vtkConeSource
from vtk import vtkDataSetMapper
from PySide.QtCore import Signal
class SurfacePicker(Picker, Intera... | berendkleinhaneveld/Registrationshop | ui/transformations/SurfacePicker.py | Python | mit | 3,129 | [
"VTK"
] | c6f9eaf24a1c30128b036c4adfb22f27068b0020357c855a7bc1aa7499f70622 |
# -*- coding: utf-8 -*-
#
# tsodyks_facilitating.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 Li... | weidel-p/nest-simulator | pynest/examples/tsodyks_facilitating.py | Python | gpl-2.0 | 5,621 | [
"NEURON"
] | 08fc69bc8ccedea6fec24743904ce0491a1468358c94dbb329ee9ee7fbe22138 |
#!/usr/bin/env python
'''
Transition density matrix and transition dipole for CASSCF/CASCI wavefunction
'''
from functools import reduce
import numpy
from pyscf import gto, scf, mcscf, fci
mol = gto.M(atom='''
C 1.20809735, 0.69749533, 0.00000000
C 0.00000000, 1.39499067, 0.00000000
C -1.20809735, ... | sunqm/pyscf | examples/1-advanced/030-transition_dipole.py | Python | apache-2.0 | 2,638 | [
"PySCF"
] | 380343cfbfaba3ef5e3aa453572ecce24085a3fcf5cf16d9dcba52cb1d16f95d |
########################################################################
# This demo illustrates voltage clamp on a soma model.
# Copyright (C) Upinder S. Bhalla, NCBS, 2018.
# This program is made available under the terms of GPL3.0. No warranty.
########################################################################... | BhallaLab/moose-examples | tutorials/Rdesigneur/ex3.1_squid_vclamp.py | Python | gpl-2.0 | 859 | [
"MOOSE"
] | cf9fbe2624b335a9db326c282f172f7d48cc786666e571845c7840893d2bbd22 |
"""
Class to fit spectroscopic observations to a direct image.
The class has been designed for image slicer data where at
the moment three spectra are recorded simultaneously.
The script is flexible enough that the input can contain
either a single pointing or single plus offset positions.
Rotations are not allowed at... | sniemi/SamPy | resolve/misc/findSlitmaskPosition.py | Python | bsd-2-clause | 47,929 | [
"Galaxy"
] | 7cbd45038e09286dd2f0b4595e36a49eb8b54528c823a0ce3f03c837222855d9 |
"""!
@brief Neural Network: Hysteresis Oscillatory Network
@details Implementation based on paper @cite article::nnet::hysteresis::1.
@authors Andrei Novikov (pyclustering@yandex.ru)
@date 2014-2020
@copyright BSD-3-Clause
"""
import numpy
import matplotlib.pyplot as plt
from scipy.integrate import... | annoviko/pyclustering | pyclustering/nnet/hysteresis.py | Python | gpl-3.0 | 13,083 | [
"NEURON"
] | 9310130535c6941ea121affe2a7554b73c605ef3a7b1c622dc14d2518be80a14 |
# Audio Tools, a module and set of tools for manipulating audio data
# Copyright (C) 2007-2016 Brian Langenberger
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the Licens... | tuffy/python-audio-tools | audiotools/coverartarchive.py | Python | gpl-2.0 | 2,645 | [
"Brian"
] | ac305d814181c662d2c3a1bbd9e6e2f722f3e95e265dbf7b60599f1faba4f996 |
# This code is so you can run the samples without installing the package
import sys
import os
sys.path.insert(0, os.path.join(os.path.dirname(__file__), '..'))
#
import pyglet
import cocos
from cocos.director import director
from cocos.actions import *
from cocos.layer import *
from cocos.particle_systems import *
cl... | adamwiggins/cocos2d | test/test_particle_explosion.py | Python | bsd-3-clause | 784 | [
"Galaxy"
] | 7f6d9e13c5c0898c2894928cddf13bd5c703debd09bca93941aabc328618a754 |
"""A quick and dirty example of using Mayavi to overlay anatomy and activation.
"""
#-----------------------------------------------------------------------------
# Imports
#-----------------------------------------------------------------------------
import numpy as np
from enthought.mayavi import mlab
from fiac_ut... | yarikoptic/NiPy-OLD | examples/fiac/view_contrasts_3d.py | Python | bsd-3-clause | 2,234 | [
"Mayavi"
] | 696f2459a701f2d3239c28b983e7f954d5d98894e7c7c03e9ca67610843c5424 |
"""Testing for kernels for Gaussian processes."""
# Author: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
# Licence: BSD 3 clause
from collections import Hashable
from sklearn.externals.funcsigs import signature
import numpy as np
from scipy.optimize import approx_fprime
from sklearn.metrics.pairwise \
imp... | kashif/scikit-learn | sklearn/gaussian_process/tests/test_kernels.py | Python | bsd-3-clause | 11,813 | [
"Gaussian"
] | b5c46e005a89a36d1758e5cc6676069488b8955e97b14863c470df9cc999fbf4 |
"""An NNTP client class based on:
- RFC 977: Network News Transfer Protocol
- RFC 2980: Common NNTP Extensions
- RFC 3977: Network News Transfer Protocol (version 2)
Example:
>>> from nntplib import NNTP
>>> s = NNTP('news')
>>> resp, count, first, last, name = s.group('comp.lang.python')
>>> print('Group', name, 'ha... | PennartLoettring/Poettrix | rootfs/usr/lib/python3.4/nntplib.py | Python | gpl-2.0 | 42,769 | [
"Brian"
] | 1024964bf5ddc4522e28890c1bd07d78383e18181a9cb06e8aeb106207297696 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | magic/maps/dust/fitter.py | Python | agpl-3.0 | 23,303 | [
"Galaxy"
] | 74ac6ed7e4e830ab68e46af14baafb14f2295ad9f295cc6d3611f9498f0d4992 |
# (c) 2014, Brian Coca, Josh Drake, et al
#
# This file is part of Ansible
#
# Ansible is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
... | wulczer/ansible | lib/ansible/cache/redis.py | Python | gpl-3.0 | 3,386 | [
"Brian"
] | 5c81254d3c1d8935431186f9efd812eda3eb80e672d4e93b3456563a0c6c3dd7 |
# Copyright 2015 The TensorFlow Authors. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applica... | aselle/tensorflow | tensorflow/python/ops/image_ops_impl.py | Python | apache-2.0 | 108,034 | [
"Gaussian"
] | cb40c4a0d48092b2d8b1267eeba5c2e6d6281105ffc80f30be9b4695e8e5a355 |
# coding=utf-8
# --------------------------------------------------------------------------
# Copyright (c) Microsoft Corporation. All rights reserved.
# Licensed under the MIT License. See License.txt in the project root for license information.
# Code generated by Microsoft (R) AutoRest Code Generator.
# Changes may ... | Azure/azure-sdk-for-python | sdk/media/azure-mgmt-media/azure/mgmt/media/models/_azure_media_services_enums.py | Python | mit | 40,552 | [
"Gaussian"
] | c77faef8303870a836decb31d93a93c60368821594338c3bdb2bf9b411ac71b3 |
from Mikado._transcripts.scoring_configuration import SizeFilter
from Mikado.scales.assignment import Assigner
import itertools
from Mikado import utilities
from Mikado.parsers.GFF import GffLine
from Mikado.loci import Transcript
from ..loci.locus import Locus, pad_transcript
from ..parsers.bed12 import BED12
from ..s... | lucventurini/mikado | Mikado/tests/test_modifications.py | Python | lgpl-3.0 | 16,062 | [
"pysam"
] | 746d0f3706f4504660d700fc3a715870775ece15930af914e7ff546627cb4e8b |
import json
import requests
def response(code):
return {
'statusCode': code,
'headers': { 'Content-Type': 'application/json' }
}
def handler(event, context):
body = event.get('body')
if not body:
body = event
else:
body = json.loads(event['body'])
if len(body)... | nbari/aws | lambda/python-lambda-proxy/test.py | Python | bsd-3-clause | 702 | [
"Elk"
] | 81fbd94b585b5ed88b46d636851d069adea631fdd7a979bd31f4da343f759a6e |
"""Guess the MIME type of a file.
This module defines two useful functions:
guess_type(url, strict=True) -- guess the MIME type and encoding of a URL.
guess_extension(type, strict=True) -- guess the extension for a given MIME type.
It also contains the following, for tuning the behavior:
Data:
knownfiles -- list ... | warner83/micropython | tests/bytecode/pylib-tests/mimetypes.py | Python | mit | 20,531 | [
"NetCDF"
] | db456cf94fc59dc159c13a5edad363023643c7f45e57211328abd8caae85d335 |
# 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 | smurf/smurf_utils.py | Python | apache-2.0 | 52,230 | [
"Gaussian"
] | 06a81a2f09277e27718c7fb0c625556eac49a17e7fbc3cf05278ca35a8d06e17 |
# ##### BEGIN GPL LICENSE BLOCK #####
#
# This program is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation; either version 2
# of the License, or (at your option) any later version.
#
# This program is distrib... | pawkoz/dyplom | blender/release/scripts/startup/bl_ui/space_sequencer.py | Python | gpl-2.0 | 40,382 | [
"Gaussian"
] | 4dc5027bbb4fde4b62325fbfadc1d030d635995a8ae2b1335940acc970692fe4 |
import os
import sys
import platform
import logging
from collections import OrderedDict
from typing import Optional, List
import archinfo
from archinfo.arch_soot import ArchSoot
from .address_translator import AT
from .utils import ALIGN_UP, key_bisect_floor_key, key_bisect_insort_right
__all__ = ('Loader',)
l = lo... | angr/cle | cle/loader.py | Python | bsd-2-clause | 49,680 | [
"VisIt"
] | 7f63814859ec2bfe58f8da68ed588d3b76056ed928e50a23d1e26c2de6594480 |
# Copyright Iris contributors
#
# This file is part of Iris and is released under the LGPL license.
# See COPYING and COPYING.LESSER in the root of the repository for full
# licensing details.
"""
Unit tests for :func:`iris.fileformats.netcdf.parse_cell_methods`.
"""
# import iris tests first so that some things can ... | pp-mo/iris | lib/iris/tests/unit/fileformats/netcdf/test_parse_cell_methods.py | Python | lgpl-3.0 | 5,108 | [
"NetCDF"
] | ee1e81d2970afe51472a57a2a5c730239427e2ae0e502e1ad718e0e494e6acb8 |
'''
Comparison of basis data against authoritative sources
'''
from ..api import get_basis
from ..misc import compact_elements
from ..sort import sort_shells, sort_potentials
from ..lut import element_sym_from_Z
from .. import manip
from ..readers import read_formatted_basis_file
from .compare import _reldiff
def _p... | MOLSSI-BSE/basis_set_exchange | basis_set_exchange/curate/compare_report.py | Python | bsd-3-clause | 9,376 | [
"Gaussian"
] | 27022b3473a43b25c11406d310b685950d8dde00279137aa4739280e1c2d6cc4 |
"""
This module defines a simplified interface for generating ABINIT input files.
Note that not all the features of Abinit are supported by BasicAbinitInput.
For a more comprehensive implementation, use the AbinitInput object provided by AbiPy.
"""
import abc
import copy
import json
import logging
import os
from colle... | materialsproject/pymatgen | pymatgen/io/abinit/inputs.py | Python | mit | 45,286 | [
"ABINIT",
"NetCDF",
"pymatgen"
] | 1aec2bc6a351aec4616fb62d34cd77623079f479b8a42232fff8d8043a76df12 |
#!/usr/bin/env python
"""This scripts allows the user to make FEP calculations along a
reaction coordinate with the AMBER and GAUSSIAN software packages"""
# qt modules
import atoms
import gaussian
import amber
# other modules
import argparse
import decimal
import matplotlib.pyplot as plt
import numpy as np
import o... | eduardoftoliveira/qt_scripts | scripts/fep.py | Python | gpl-3.0 | 19,931 | [
"Amber",
"Gaussian"
] | 5cefe3a3a1ad0b22a3e47f5e00a0c169240b9fb6aad788067d9dcc0cd845929e |
# $Id$
#
# Copyright (C) 2003-2006 greg Landrum and 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.
#
""" Supplies a class fo... | rdkit/rdkit-orig | rdkit/Chem/Fingerprints/DbFpSupplier.py | Python | bsd-3-clause | 4,222 | [
"RDKit"
] | ab6504be18b67f2d5c2487821d542906f44600de7882fc8f64032abf3c20faec |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
import os
import warnings
from pymatgen.core.structure import Structure
from pymatgen.core.units import Ha_to_eV, bohr_to_ang
from pymatgen.io.abinit.abiobjects import *
from pymatgen.util.testing import Pymat... | gmatteo/pymatgen | pymatgen/io/abinit/tests/test_abiobjects.py | Python | mit | 7,479 | [
"ABINIT",
"pymatgen"
] | 868a3851fb7466eeb98b8f17201f11a748be2bedbd7c12239f580deba26c8acf |
import random
import time
import src.obj
import src.utils
import src.entities
def personInteraction():
entities.player.location = entities.getLocation('Interact')
personType = random.randint(1, 3)
if personType == 1:
person = [random.choice(entities.enemies), random.choice(entities.weapons)]
... | DaVinci789/textbasedgame | src/locations.py | Python | gpl-3.0 | 10,386 | [
"VisIt"
] | 6b8b74b7d1559261f2819669409b11656a26ddc6de38f44f0aa65b822a144a6f |
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Matti Hamalainen <msh@nmr.mgh.harvard.edu>
# Denis A. Engemann <denis.engemann@gmail.com>
#
# License: BSD (3-clause)
import copy as cp
import os
from math import floor, ceil, log
import itertools as itt
import warnings
import ... | lorenzo-desantis/mne-python | mne/cov.py | Python | bsd-3-clause | 71,951 | [
"Gaussian"
] | 70fccf679a7551af0b6ae51e7cf3ea35978530860406ea0bdfcfb0d53c00141d |
#!/usr/bin/python
# This was written for educational purpose only. Use it at your own risk.
# Author will be not responsible for any damage!
# !!! Special greetz for my friend sinner_01 !!!
# !!! Special thanx for d3hydr8 and rsauron who inspired me !!!
#
# In version 2 added proxy support
#
##########################... | knightmare2600/d4rkc0de | others/lfi-rfi.py | Python | gpl-2.0 | 6,219 | [
"VisIt"
] | 13010ca685f7992691a76b1caf1cff68efaa858458064cc5fc2241f3d45f88bb |
# Copyright (c) 2012 Santosh Philip
# =======================================================================
# Distributed under the MIT License.
# (See accompanying file LICENSE or copy at
# http://opensource.org/licenses/MIT)
# =======================================================================
"""functions t... | eayoungs/eppy | eppy/modeleditor.py | Python | mit | 31,102 | [
"EPW"
] | 92c85c9e7a765c434c9b71ae3800c8796e905049063364d7a3fd2193b0256690 |
#!/usr/bin/env python
##########################################################################
#
# Copyright 2008 Tungsten Graphics, Inc., Cedar Park, Texas.
# All Rights Reserved.
#
# Permission is hereby granted, free of charge, to any person obtaining a
# copy of this software and associated documentation files ... | ayoubg/gem5-graphics | Mesa-7.11.2_GPGPU-Sim/src/gallium/tools/trace/model.py | Python | bsd-3-clause | 5,701 | [
"VisIt"
] | de0ba4bdb97e4722fc01e9dfeb0ccfe4eabc53fe436f68001bd6ce782fd0371e |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Fri Apr 28 13:33:45 2017
@author: Bereket Abraham
"""
from keras.models import Sequential, Model
from keras.layers import Flatten, Dense, BatchNormalization, Dropout, Reshape, Permute, Activation, Input
from keras.layers.convolutional import Convolution2D,... | babraham123/deepdriving | new/train_combined.py | Python | mit | 8,675 | [
"Gaussian"
] | e634709d2ca50afcbaa2a1efc4e7fb2dd88f05fee49974b3a17dc8093c411040 |
#INFORMATION
#The input of this script is a pandas dataframe containing the ab-initio data_path
#Under the PARAMETERS section the descriptor and training method can be defined
#The output is a dataframe that contains the predicted energies as well as the trained model
#(the trained model is accesible trough the metadat... | CondensedOtters/PHYSIX_Utils | Projects/Aertgeerts_2019/Zundel-KRR/2_model_training/model_trainer.py | Python | gpl-3.0 | 15,541 | [
"ASE"
] | 430dcec1f1e2c2eef7310262aea98439b4f19e94659813cf2881a0320d0e2faa |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
'''
Modified parameters file for the Hybrid LFP scheme, applying the methodology with
the model of:
Potjans, T. and Diesmann, M. "The Cell-Type Specific Cortical Microcircuit:
Relating Structure and Activity in a Full-Scale Spiking Network Model".
Cereb. Cortex (2014) 24 (... | espenhgn/hybridLFPy | examples/Hagen_et_al_2016_cercor/cellsim16popsParams_modified_ac_input.py | Python | gpl-3.0 | 39,517 | [
"Gaussian",
"NEURON"
] | aa00ccf5228f972494ff5c0376a64cd04cd02f3a33799268c586e54ebf1a2ee3 |
#!/usr/bin/env python
#partest = True
import gc
import sys
import time
import numpy as np
from ase.units import Bohr
from ase.utils.memory import MemorySingleton, MemoryStatistics
from gpaw.mpi import world, distribute_cpus
from gpaw.utilities import gcd
#from gpaw.utilities.tools import tri2full, md5_array, gram_sc... | qsnake/gpaw | gpaw/test/parallel/ut_kptops.py | Python | gpl-3.0 | 8,873 | [
"ASE",
"GPAW"
] | 7b0447568fa6b47ffd8effe7c7d8d072e11a36d8893292a32616beda95144ec0 |
import logging
from cis.data_io.products import AProduct
from cis.data_io.netcdf import get_data, get_metadata, read_many_files_individually
from iris.coords import DimCoord, AuxCoord
from iris.cube import Cube
from cis.data_io.gridded_data import GriddedData
import cis.utils as utils
from cis.time_util import cis_stan... | duncanwp/cis_plugins | HSRL2.py | Python | lgpl-3.0 | 4,262 | [
"NetCDF"
] | 5795ff0e0cb35b76658f39df66af5aad0de0a41b3ab6ca068b4799fb001b45c0 |
"""
This sample demonstrates an implementation of the Lex Code Hook Interface
in order to serve a sample bot which manages orders for stocks.
Bot, Intent, and Slot models which are compatible with this sample can be found in the Lex Console
as part of the 'Orderstocks' template.
For instructions on how to set up and t... | gpaw789/wolfbot-lex | WolfBot_Watchlist_Show/WolfBot_Spotcheck.py | Python | gpl-3.0 | 10,201 | [
"VisIt"
] | 5cf08cfbd1b1e0b3ff90501d0d532bda0897861ebf8ad823c34f08ded25c63be |
# Copyright (C) 2002, Thomas Hamelryck (thamelry@binf.ku.dk)
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
import numpy
from Bio.SVDSuperimposer import SVDSuperimposer
from Bio.PDB.PDBExceptions i... | NirBenTalLab/proorigami-cde-package | cde-root/usr/lib64/python2.4/site-packages/Bio/PDB/Superimposer.py | Python | mit | 2,332 | [
"Biopython"
] | f77f974a8af3b39f62e9283bc78231b37d88db371291f8cc752a03ae44cd1828 |
# /usr/local/bin/python3
# -*- coding: utf-8 -*-
# __author__ = 'Jieer'
#__version__ = '1.0'
empty_list = []
weekdays = ['Monday','Tuesday','Wednesday','Thursday','Friday']
another_empty_list = list()
print(len(weekdays))
print(list('Jieer'))
a_tuple = ('ready','aim','fire')
list_tuple = list(a_tuple)
print(list... | lmee/exercise1 | list_tuple_dict.py | Python | apache-2.0 | 2,245 | [
"MOE"
] | 75b5cdaa2626d676aa8d28e66603696410b82f28c14f3a3016b81b85cf0272d6 |
#!/usr/bin/python
# TODO - python path - assuming condo here
## HEALTH WARNING - BETA CODE IN DEVELOPMENT ##
'''
This standalone application will build a mesh from a nifti classification file.
To keep the procedure as similar as possible to the way mrMesh used to do this,
we will keep this as a standalon applicatio... | andregouws/mrMeshPy | matlabRoutines/pyMeshBuild_ImageData.py | Python | mit | 9,150 | [
"VTK"
] | 0b2c68d103c48c2afb0dfc040589ff7a66e60cf8d26413124eb1987471a9b2e0 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
'''
freeseer - vga/presentation capture software
Copyright (C) 2013 Free and Open Source Software Learning Centre
http://fosslc.org
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 ... | Freeseer/freeseer | src/freeseer/plugins/videomixer/videopassthrough/widget.py | Python | gpl-3.0 | 3,968 | [
"VisIt"
] | 6b2c1964c64c33ead554d3ffbdba985a2394d57a380413f855c19abcf8b9acb0 |
"""Unpacking archives of various formats."""
# Copyright (C) 2009, Thomas Leonard
# See the README file for details, or visit http://0install.net.
from zeroinstall import _, logger
import os, sys, subprocess
import shutil
import glob
import traceback
from tempfile import mkdtemp, mkstemp
import re
import errno
from z... | rammstein/0install | zeroinstall/zerostore/unpack.py | Python | lgpl-2.1 | 20,377 | [
"VisIt"
] | e26646c5eec73a8533d56585312761cdca64b736d8cc76729a6e86053d681da7 |
import sys
import os
from os import listdir
from os.path import isfile, join
from cx_Freeze import setup, Executable
import cx_Freeze.hooks
def hack(finder, module):
return
cx_Freeze.hooks.load_matplotlib = hack
import scipy
import matplotlib
from encodings import ascii
from encodings import idna
from encodings imp... | JannickWeisshaupt/OpenDFT | src/build_freeze.py | Python | gpl-3.0 | 4,483 | [
"pymatgen"
] | aa05caa305cfb28a16cf3c7fb1e2664cb57408d9b56028416be82e0105f67a58 |
# coding=utf-8
# Copyright 2014 Pants project contributors (see CONTRIBUTORS.md).
# Licensed under the Apache License, Version 2.0 (see LICENSE).
from __future__ import (absolute_import, division, generators, nested_scopes, print_function,
unicode_literals, with_statement)
from textwrap import... | cevaris/pants | tests/python/pants_test/backend/docgen/targets/test_wiki_page.py | Python | apache-2.0 | 3,738 | [
"exciting"
] | 8746ef06db42be1300fb947b496b79a623cab722b3c6e871d5192ac2d6730978 |
"""This module contains various functions that are special cases
of incomplete gamma functions. It should probably be renamed.
"""
from ...core import (Add, EulerGamma, Function, I, Integer, Pow, Rational,
cacheit, expand_mul, oo, pi, zoo)
from ...core.function import ArgumentIndexError
from ...co... | diofant/diofant | diofant/functions/special/error_functions.py | Python | bsd-3-clause | 64,169 | [
"Gaussian"
] | 52f10c1e4bf5431274766be89a4a66d4e50d466051199ab77ee7be3795211930 |
from __future__ import print_function
from future.utils import iteritems
import pytest
import xarray as xr
import numpy as np
# example from comodo website
# https://web.archive.org/web/20160417032300/http://pycomodo.forge.imag.fr/norm.html
# netcdf example {
# dimensions:
# ni = 9 ;
# ... | rabernat/xgcm | xgcm/test/datasets.py | Python | mit | 13,360 | [
"NetCDF"
] | 5329775e244326fce3c7afdb45cc6061d9adc37f84bd5a82883a045c8d4539f2 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | tmerrick1/spack | var/spack/repos/builtin/packages/trilinos/package.py | Python | lgpl-2.1 | 32,051 | [
"NetCDF"
] | 15291964841d38bb97ae4f61ee338d585664dfdbae373dd9cdcbea46898aacb8 |
"""
This module contains code for a GUI frontend for searches
"""
import os
from tkinter import *
from tkinter import ttk, filedialog, messagebox
from bin.initialize_goat import configs
from util import util
from searches import search_obj
from results import intermediate
from gui.util import input_form, gui_util
fr... | chris-klinger/Goat | gui/searches/search_gui.py | Python | gpl-3.0 | 27,333 | [
"BLAST"
] | 6906c2319677b37a3645524112570776fe2693190922d25684f65f706fac1515 |
#!/usr/bin/env python3
# Copyright (C) 2016-2017(H)
# Max Planck Institute for Polymer Research
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, eit... | espressopp/espressopp | examples/electrostatics/electrostatics_example.py | Python | gpl-3.0 | 10,133 | [
"CRYSTAL",
"ESPResSo",
"VMD"
] | 950bad84f3411b9df43b099c371d24739aa517e0002e4b2c2ba1b84c8e956699 |
# glviewloader.py ---
#
# Filename: loadcell.py
# Description:
# Author: Subhasis Ray
# Maintainer:
# Created: Thu Feb 4 20:34:34 2010 (+0530)
# Version:
# Last-Updated: Fri Feb 5 18:01:32 2010 (+0530)
# By: Subhasis Ray
# Update #: 126
# URL:
# Keywords:
# Compatibility:
#
#
# Commentary:
#... | BhallaLab/moose-thalamocortical | pymoose/gui/qt/glviewloader.py | Python | lgpl-2.1 | 3,586 | [
"MOOSE"
] | 10ed971bec10507e3e7a8710c9e59184410d98b4cff2496ff50fb63905f67025 |
# -*- coding: utf-8 -*-
"""
Generate centreline and write it out as .vtk legacy format.
"""
import os
import sys
# Run in current directory.
os.chdir(os.path.dirname(os.path.abspath(__file__)))
# Import path for the CentrelineGenerator script.
importPath = os.path.abspath(os.path.join(os.path.dirname(__file__), '../... | BlueFern/DBiharMesher | tmpData/c8064.thin/Generate8064Centreline.py | Python | gpl-2.0 | 1,019 | [
"VTK"
] | 8557e0c5185718c5b39236721b37d8a5d949d80b667a3213ce667f833874dd2f |
# -*- coding: utf-8 -*-
from __future__ import absolute_import, division, print_function, unicode_literals
from six.moves import zip, map
import six
import dtool
import utool as ut
import vtool as vt
import pyflann
import numpy as np
from ibeis.control.controller_inject import register_preprocs, register_subprops
(prin... | SU-ECE-17-7/ibeis | ibeis/new_annots.py | Python | apache-2.0 | 49,277 | [
"Gaussian"
] | 59ac3e4027e4f98a541ddf90324d8dd3b463e4d9044d08fe6e7e8b68fd9ed1cc |
#
# Copyright (C) 2017-2018 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... | hmenke/espresso | testsuite/python/subt_lj.py | Python | gpl-3.0 | 1,870 | [
"ESPResSo"
] | d1e9b4c435195629d255c9fe156b2d14afef5c2ef6d7451f50e1d28629a340d1 |
#------------------------------------------------------------------------------
# Copyright (c) 2007, Enthought, Inc.
# All rights reserved.
#
# This software is provided without warranty under the terms of the BSD
# license included in enthought/LICENSE.txt and may be redistributed only
# under the conditions describe... | enthought/etsproxy | enthought/util/distribution/gaussian.py | Python | bsd-3-clause | 1,089 | [
"Gaussian"
] | 439d7105bc3d67d2d2e16f2b8c4039889c9944f66a47cf4b56e8bd3548a7e0d5 |
from __future__ import with_statement
"""
Simple two-dimensional mathematical or geometrical pattern generators.
$Id$
"""
__version__='$Revision: 10131 $'
from math import pi, sin, cos, sqrt
import numpy
from numpy.oldnumeric import around,bitwise_and,sin,add,Float,bitwise_or
from numpy import alltrue
from .. impor... | jesuscript/topo-mpi | contrib/basic.py | Python | bsd-3-clause | 38,946 | [
"Gaussian"
] | 9ef33e563be50e4cbe5b2e0ff6b3d067af745527b060aabc053b43e7339eb52e |
# #
# Copyright 2009-2021 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 | easybuild/framework/easyconfig/easyconfig.py | Python | gpl-2.0 | 125,722 | [
"NetCDF"
] | af66bdd861ef62bfacabc21729d8b2d57eaf910c261b7451e4ab3ab5285e637e |
r"""XML-RPC Servers.
This module can be used to create simple XML-RPC servers
by creating a server and either installing functions, a
class instance, or by extending the SimpleXMLRPCServer
class.
It can also be used to handle XML-RPC requests in a CGI
environment using CGIXMLRPCRequestHandler.
The Doc* classes can b... | kenshay/ImageScript | Script_Runner/PYTHON/Lib/xmlrpc/server.py | Python | gpl-3.0 | 37,349 | [
"Brian"
] | 643f1890ab45e41412d35ea88e2a55c29b8e88694b3075e4013d7fe42ee6fe11 |
# coding: utf-8
# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
import os
from shutil import rmtree
from tempfile import mkdtemp
from nipype.testing import (assert_equal, assert_raises, skipif,
assert_almost_equal, example_d... | sgiavasis/nipype | nipype/algorithms/tests/test_mesh_ops.py | Python | bsd-3-clause | 2,877 | [
"VTK"
] | 86024a2459f9002bcf1f0d5bdbb49a0c4f9bfaf301d482a699373577ef86e406 |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# ... | SKIRT/PTS | modeling/config/parameters.py | Python | agpl-3.0 | 12,902 | [
"Galaxy"
] | 3d027e6a7b4b0f5ded6f1f56691fd854ce62618fbef63053ae83c027bb8fc772 |
import logging
import numpy as np
import os
import pkg_resources
from pprint import pformat
import scipy
from scipy.ndimage.morphology import generate_binary_structure, iterate_structure
import caiman.utils.utils
from ...paths import caiman_datadir
from .utilities import dict_compare, get_file_size
class CNMFParams(... | agiovann/Constrained_NMF | caiman/source_extraction/cnmf/params.py | Python | gpl-2.0 | 50,157 | [
"Gaussian",
"NEURON"
] | ac9c00b61a169e20bb2a7d99b5cf60a4c751969c36d897879335d39e9492abf0 |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__email__ = "shyuep... | xhqu1981/pymatgen | pymatgen/util/tests/test_string_utils.py | Python | mit | 2,162 | [
"pymatgen"
] | 792412fdba42451e967683339aa957d5047706a5fc63c283388f1ff0b3f7a111 |
"""
Created on 06.07.2014
@author: JDC Chodera, JH Prinz
"""
import logging
import time
import openpathsampling as paths
from openpathsampling.netcdfplus import NetCDFPlus, WeakLRUCache, ObjectStore, \
ImmutableDictStore, NamedObjectStore, PseudoAttributeStore
from .stores import SnapshotWrapperStore
import op... | choderalab/openpathsampling | openpathsampling/storage/storage.py | Python | lgpl-2.1 | 17,720 | [
"NetCDF",
"OpenMM"
] | af331f9ed42175e9a16cfd55d665d7c78ded97e4c333d1c2abe9f35229620cb3 |
#!/usr/bin/env python
########################################################################
# $HeadURL$
# File : dirac-fix-mysql-script
# Author : Ricardo Graciani
########################################################################
"""
Fixes the mysql.server script, it requires a proper /LocalInstallation s... | petricm/DIRAC | Core/scripts/dirac-fix-mysql-script.py | Python | gpl-3.0 | 1,044 | [
"DIRAC"
] | c8627dade644f09f888b415408ec89e560a268e9b30eaf01650236b2eeb006ad |
"""
Install file for SciTokens project.
"""
import os.path
import re
import setuptools
def find_version(path, varname="__version__"):
"""Parse the version metadata variable in the given file.
"""
with open(path, 'r') as fobj:
version_file = fobj.read()
version_match = re.search(
r"^... | scitokens/scitokens | setup.py | Python | apache-2.0 | 1,402 | [
"Brian"
] | 48c35c5ee99edcfbf1d42acfdeccbd230e9805ef9cac5a8a33ad6b0e8cca37cc |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
"""
This module defines classes for point defect transformations on structures
"""
__author__ = "Bharat Medasani"
__copyright__ = "Copyright 2014, The Materia... | czhengsci/pymatgen | pymatgen/transformations/defect_transformations.py | Python | mit | 11,308 | [
"pymatgen"
] | 2a12696bf83b5f6d27e446dde32d37051b645adfe527027a865d38c52539eab1 |
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from datetime import datetime
import re
import traceback
import warnings
import numpy as np
import pandas as pd
from collections import defaultdict
try:
from pandas.errors import OutOfBoundsDatetime
except ... | jhamman/xray | xarray/conventions.py | Python | apache-2.0 | 41,624 | [
"NetCDF"
] | 98f43f0dbd6863a232b157f0c030fe0eb92e5ce959f70b1b53a57b858da0a595 |
# -*- coding: utf-8 -*-
#******************************************************************************
# FILE: rout_vic.py
# AUTHOR: Kel Markert
# EMAIL: kel.markert@nasa.gov
# ORGANIZATION: NASA-SERVIR, UAH/ESSC
# MODIFIED BY: n/a
# CREATION DATE: 28 Oct. 2016
# LAST MOD DATE: 03 Apr. 2017
# PURPOSE: This script runo... | KMarkert/servir-vic-training | scripts/rout_vic.py | Python | gpl-3.0 | 9,161 | [
"NetCDF"
] | 9676868dc892c855fb5a62638d4f03c197cc678d0316c248064b00140be7ec0b |
"""Test generation helpers
Intended to functionalize common tasks when working with the pytest_generate_tests hook.
When running a test, it is quite often the case that multiple parameters need to be passed
to a single test. An example of this would be the need to run a Provider Add test against
multiple providers. W... | Yadnyawalkya/integration_tests | cfme/utils/testgen.py | Python | gpl-2.0 | 14,164 | [
"VisIt"
] | 3064461f96a9958fd8a6612d6845d1235f93273631f59d8121505b30a408f151 |
import os
import datetime
from nxtools import log_traceback, xml, logging
from firefly.api import api
from firefly.core.enum import ObjectStatus, ContentType, MediaType, JobState
from firefly.common import pixlib
from firefly.objects import Event, Item
from firefly.base_module import BaseModule
from firefly.widgets i... | immstudios/firefly | firefly/modules/scheduler.py | Python | gpl-3.0 | 9,163 | [
"Firefly"
] | 12ff1deb2d557100e07f17e9a56a8f58262fb1638fee7a5ea64d067837cf9b10 |
from contextlib import contextmanager
from json import load
from os import makedirs
from os import unlink
from os.path import exists
from os.path import abspath
from os.path import dirname
from os.path import join
from os.path import basename
from os.path import sep
import fnmatch
from re import compile
from re import ... | ssorgatem/pulsar | pulsar/client/action_mapper.py | Python | apache-2.0 | 25,340 | [
"Galaxy"
] | 461ada2d672439f3b2a020213012bc6055013c5ed6807c39e717583f4d48bdc8 |
##############################################################################
# Copyright (c) 2013-2018, Lawrence Livermore National Security, LLC.
# Produced at the Lawrence Livermore National Laboratory.
#
# This file is part of Spack.
# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved.
# LLNL-CODE-64... | tmerrick1/spack | var/spack/repos/builtin/packages/netcdf-cxx4/package.py | Python | lgpl-2.1 | 2,033 | [
"NetCDF"
] | 8198571059007bbcbc2793448345a1a44a2fc76bc5f12b2e665806580c1a8e1d |
# 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 u... | tqchen/tvm | python/tvm/relay/frontend/change_datatype.py | Python | apache-2.0 | 3,475 | [
"VisIt"
] | d682819fd4c66ebf5c06f375fe6b7e92f6fc6f76046aa60ef61b295df2c95277 |
# Copyright (C) 2014 Pierre de Buyl
# Copyright (C) 2012,2013
# Max Planck Institute for Polymer Research
# Copyright (C) 2008,2009,2010,2011
# Max-Planck-Institute for Polymer Research & Fraunhofer SCAI
#
# This file is part of ESPResSo++.
#
# ESPResSo++ is free software: you can redistribute it and... | junghans/espressopp | src/analysis/TotalVelocity.py | Python | gpl-3.0 | 2,730 | [
"ESPResSo"
] | fa705d4bf490e829841f6ba354bf71486461d4056d58f6f7d29b0de128b90efa |
#! /usr/bin/python
import math
import visualizer
import statistics
import numpy as np
from datagen import constructData
from sklearn import gaussian_process
# Applies Gaussian Processes to the electricity dataset,
# prints out the accuracy rate to the terminal and plots
# predictions against actual values
def gaussia... | lbenning/Load-Forecasting | src/gpr.py | Python | mit | 2,932 | [
"Gaussian"
] | ed669bdb0e39923f225ac0ac3b42fcc742bd718208d9421874723f212211b402 |
#
#@BEGIN LICENSE
#
# PSI4: an ab initio quantum chemistry software package
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later ver... | spring01/libPSI | src/lib/libfunctional/matlab/mfiles/purify.py | Python | gpl-2.0 | 3,386 | [
"Psi4"
] | 35e6cab689af946084a3f9c9f6fab4bf87cbb2354d1ff1b0aa8ee593138c8880 |
#!/bin/env python
"""
Compute forces of the supercell system created by phonopy and
create FORCE_SETS file, which includes forces on atoms.
Usage:
pmd2phonopy.py [options] PMDINI
Options:
-h, --help Show this help message and exit.
-c, --cutoff=CUTOFF
Cutoff radius of the interatomic pote... | ryokbys/nap | nappy/pmd/pmd2phonopy.py | Python | mit | 4,893 | [
"phonopy"
] | 8fd2528239d4a34fe91d45d2ee378e4a9c429c4b84b703f38c3cb4707a21e562 |
tutorial_tests = """
Let's try a simple generator:
>>> def f():
... yield 1
... yield 2
>>> for i in f():
... print(i)
1
2
>>> g = f()
>>> next(g)
1
>>> next(g)
2
"Falling off the end" stops the generator:
>>> next(g)
Traceback (most recent call last... | invisiblek/python-for-android | python3-alpha/python3-src/Lib/test/test_generators.py | Python | apache-2.0 | 50,158 | [
"VisIt"
] | b85b7da5a8dd94aa36fa2302fcb333ec7bd5182949554b919fefe67cb4c1319f |
import pysam
import csv
def get_new_row(orig_bam, new_bam, row):
assert '1/1' in row['DGRP-362'] or '1/1' in row['DGRP-765']
# Check that we actually have a SNP here - i.e. the fastas will have
# different bases at this position
if '1/1' in row['DGRP-362'] and '1/1' in row['DGRP-765']:
retur... | d-quinn/bio_quinn2013 | parental_alignment/combining_SNPs_with_vcf.py | Python | mit | 4,780 | [
"pysam"
] | da344a37725d1bc15a1fdae1e992555f67efbe137fe59fdffc9146d0c79b11ec |
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