text stringlengths 12 1.05M | repo_name stringlengths 5 86 | path stringlengths 4 191 | language stringclasses 1
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# Copyright 2016 the GPflow authors
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writin... | GPflow/GPflow | tests/gpflow/models/test_methods.py | Python | apache-2.0 | 3,160 | [
"Gaussian"
] | 733ee74c764de2021b51ff229f0293ab96dd043b11b4d8df8c6d07d4237b4af8 |
"""
@name: PyHouse/src/Modules/_test/test_Scheduling.py
@author: D. Brian Kimmel
@contact: D.BrianKimmel@gmail.com
@copyright: (c) 2015-2018 by D. Brian Kimmel
@license: MIT License
@note: Created on Jul 31, 2015
@Summary:
"""
__updated__ = '2019-07-29'
from twisted.trial import unittest, reporter, ... | DBrianKimmel/PyHouse | Project/src/Modules/House/_test/test_Scheduling.py | Python | mit | 769 | [
"Brian"
] | cf0ee9ab8ba251414d14263eef0227af950c9ba84774f9e253423f5bcc3b75b9 |
#!/usr/bin/env python
# The contents of this file are subject to the BitTorrent Open Source License
# Version 1.1 (the License). You may not copy or use this file, in either
# source code or executable form, except in compliance with the License. You
# may obtain a copy of the License at http://www.bittorrent.com/li... | galaxy001/libtorrent | BitTorrent-4.4.0/bittorrent.py | Python | mit | 145,556 | [
"VisIt"
] | 5eb7f4ade57f33e366f0eec7e957d4e4f5e3dfabe4be0c64d28f6ea07018c359 |
import numpy as np
try:
import scipy.optimize as opt
except ImportError:
pass
from ase.optimize.optimize import Optimizer
class Converged(Exception):
pass
class OptimizerConvergenceError(Exception):
pass
class SciPyOptimizer(Optimizer):
"""General interface for SciPy optimizers
Only the ca... | suttond/MODOI | ase/optimize/sciopt.py | Python | lgpl-3.0 | 10,601 | [
"ASE"
] | 434eb7b1f2bf6a49ee9f72f8648cb1076edb1577a195a729abdfc4d3350ab5cc |
# Copyright 2013 by Christian Brueffer. All rights reserved.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Command line wrapper for the multiple sequence alignment program MSAProbs.
"""
from _... | updownlife/multipleK | dependencies/biopython-1.65/build/lib.linux-x86_64-2.7/Bio/Align/Applications/_MSAProbs.py | Python | gpl-2.0 | 3,498 | [
"Biopython"
] | 05d4ec12d5c02db6ac357322ca551950a3107ed3462b39c6eebcaa77fdf73d70 |
"""
Support the ISY-994 controllers.
For configuration details please visit the documentation for this component at
https://home-assistant.io/components/isy994/
"""
import asyncio
from collections import namedtuple
import logging
from urllib.parse import urlparse
import voluptuous as vol
from homeassistant.core impo... | ewandor/home-assistant | homeassistant/components/isy994.py | Python | apache-2.0 | 16,941 | [
"VisIt"
] | 96b5c2a0d70977e17e7106f88e11072a88ac788c7d086c996e45944a74b84f35 |
#!/usr/bin/env python
import numpy as np
import networkx as nx
###########################
### create scatter data ###
###########################
n = 6 # specify the number of observations for each cluster
np.random.seed(42) ... | ajrichards/htsint | htsint/stats/ClusteringData.py | Python | bsd-3-clause | 4,363 | [
"Gaussian"
] | 7aabb94aa3885c5a79cb75c9e7911beb1b72d0314b1db591efe9a8e7dd3beb96 |
#
# @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 program is free software; you can redistribute it and/or modify
# it under the terms of ... | kratman/psi4public | psi4/driver/qcdb/libmintsbasissetparser.py | Python | gpl-2.0 | 12,796 | [
"Gaussian",
"Psi4"
] | cf775c85ec7c71bdbddea3cc804d5882c07b19c68ed199cc2c6e0d1c6109abb6 |
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8
#
# MDAnalysis --- https://www.mdanalysis.org
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
#... | MDAnalysis/mdanalysis | testsuite/MDAnalysisTests/coordinates/test_chemfiles.py | Python | gpl-2.0 | 8,311 | [
"Chemfiles",
"LAMMPS",
"MDAnalysis"
] | fd98e4d3ec1b31cfa0dda1238bef1cc986c3f266c2d99ce27491331c5a96c062 |
#!/usr/bin/python3
# -*- coding: utf-8 -*-
#
# Panels lib
#
# Copyright (C) 2016 Bitergia
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 3 of the License, or
# (at your option)... | sanacl/GrimoireELK | grimoire/panels.py | Python | gpl-3.0 | 14,619 | [
"Elk"
] | d88f3d71df9115d86e3c28ade4077e288befe163ad23c1f8601004ff7adadb83 |
# -*- coding: utf-8 -*-
# Form implementation generated from reading ui file 'Configurator.ui'
#
# Created by: PyQt4 UI code generator 4.11.4
#
# WARNING! All changes made in this file will be lost!
from PyQt4 import QtCore, QtGui
try:
_fromUtf8 = QtCore.QString.fromUtf8
except AttributeError:
def _fromUtf8(... | rainer85ah/VisionViewer | src/Builders/GaussianBlur/Configurator.py | Python | mit | 6,222 | [
"Gaussian"
] | 5842c691dc6dabc3fcfe2632e6931d7f59b681f5f00ec42dc16d8a80c258a13b |
"""Wigner-Seitz truncated coulomb interaction.
See:
Ravishankar Sundararaman and T. A. Arias:
Phys. Rev. B 87, 165122 (2013)
Regularization of the Coulomb singularity in exact exchange by
Wigner-Seitz truncated interactions: Towards chemical accuracy
in nontrivial systems
"""
import sys
from... | robwarm/gpaw-symm | gpaw/response/wstc.py | Python | gpl-3.0 | 2,740 | [
"ASE",
"GPAW"
] | 8982152e7113aebfcc5a95079671429125c2545c7b8c52fef857f02d5e842b98 |
#!/usr/bin/env python3
'''
Unpack ARM instruction XML files extracting the encoding information
and ASL code within it.
'''
import argparse
import glob
import json
import os
import re
import string
import sys
import xml.etree.cElementTree as ET
from collections import defaultdict
from itertools import takewhile
incl... | alastairreid/mra_tools | bin/instrs2asl.py | Python | bsd-3-clause | 39,190 | [
"VisIt"
] | b74d4be93bc6bca09ae9316397a035668411bf84e25fb50c636330d568926e0d |
#import nsdf
#import table
#import swc
#import neuroml
import moose
__all__ = ["moose"]
#"nsdf",
# "table",
# "swc",
# "neuroml",
# "moose"]
| dilawar/moogli | moogli/extensions/__init__.py | Python | gpl-2.0 | 182 | [
"MOOSE"
] | 166d73b6f5ecfc6437814a848a17ab350e3c059bc8ea484b0379e73864894ca9 |
# Copyright 2007-2009 by Peter Cock. All rights reserved.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package..
"""Bio.SeqIO support for the "genbank" and "embl" file formats.
You are expected to use ... | NirBenTalLab/proorigami-cde-package | cde-root/usr/lib64/python2.4/site-packages/Bio/SeqIO/InsdcIO.py | Python | mit | 29,113 | [
"Biopython"
] | 3e64aefe2f5c89030e9f495f6d80d55438a27b037e9bf5aefd77db5445c20f9d |
"""Test case for autocomplete implementations."""
import os
import uuid
from django import VERSION
from django.contrib.contenttypes.models import ContentType
from django.contrib.staticfiles.testing import StaticLiveServerTestCase
from django.core.urlresolvers import reverse
from django.utils import six
from splinter... | luzfcb/django-autocomplete-light | src/dal/test/case.py | Python | mit | 3,287 | [
"VisIt"
] | 18d5b21079ec1ad0f8000cb248baa7c8b4589fc2548cedeafccba1d4b69a5e71 |
import img_scale
import pyfits as pyf
import pylab as pyl
from mpl_toolkits.axes_grid1 import axes_grid
import cPickle as pickle
import os
from scipy.stats import scoreatpercentile
def mk_image(galaxy):
base = './../../images_v5/GS_2.5as_matched/gs_all_'
i_img = pyf.getdata(base+str(galaxy)+'_I.fits')
j_i... | boada/ICD | sandbox/plot_icd_examples.py | Python | mit | 2,513 | [
"Galaxy"
] | ba49c9b811cd5c3bbd79f462e9864efab00e55b1bf048f1ec4c0e3c112d5b5ab |
""" Module for converting various mesh formats."""
# Copyright (C) 2006 Anders Logg
#
# This file is part of DOLFIN.
#
# DOLFIN is free software: you can redistribute it and/or modify
# it under the terms of the GNU Lesser General Public License as published by
# the Free Software Foundation, either version 3 of the L... | maciekswat/dolfin_1.3.0 | site-packages/dolfin_utils/meshconvert/meshconvert.py | Python | gpl-3.0 | 49,645 | [
"NetCDF"
] | b89a8480d7b46c1f25c47f63f7faebd7dbd99554fc625553656d832b82925eb4 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
import rdkit
from rdkit.Chem import AllChem
from rdkit import DataStructs
__license__ = "X11"
METADATA = {
"id": "method_rdkit_fcfp2_2048_tanimoto",
"representation": "fcfp2_2048",
"similarity": "tanimoto"
}
def _compute_fingerprint(molecule):
return Al... | skodapetr/lbvs-environment | methods/fcfp/fcfp2_2048_tanimoto.py | Python | mit | 1,423 | [
"RDKit"
] | a4e9a026f8623f8d9620fa3abbb9cdf55bbc489dd5d18f3601e8554cdbfec8dd |
#!/usr/bin/env python
#
# This code was copied from the data generation program of Tencent Alchemy
# project (https://github.com/tencent-alchemy).
#
#
# #
# # Copyright 2019 Tencent America LLC. All Rights Reserved.
# #
# # Licensed under the Apache License, Version 2.0 (the "License");
# # you may not use this file e... | gkc1000/pyscf | pyscf/df/hessian/uhf.py | Python | apache-2.0 | 25,334 | [
"PySCF"
] | 5cab8ab8908106463f93cf3a25caee6a5d58d26d411a2fa329226e02608e8fa1 |
# class generated by DeVIDE::createDeVIDEModuleFromVTKObject
from module_kits.vtk_kit.mixins import SimpleVTKClassModuleBase
import vtk
class vtkImageMedian3D(SimpleVTKClassModuleBase):
def __init__(self, module_manager):
SimpleVTKClassModuleBase.__init__(
self, module_manager,
vtk.... | nagyistoce/devide | modules/vtk_basic/vtkImageMedian3D.py | Python | bsd-3-clause | 489 | [
"VTK"
] | 3a0a6ada2f74f638045148dd425d5bf4c127ff8347a0b602b10bf39cf8281c2f |
#!/usr/bin/env python
from data.electron_configuration import configurations, core_states
from ase.units import Ha
import copy
from data.ONCV_PBEsol_conf import ONCV_PBEsol_conf
class econf():
def __init__(self, symbol):
"""
reference electronic configuration of elements.
"""
self.... | mailhexu/pyDFTutils | resource/phonon_ana/pyFA/psp.py | Python | lgpl-3.0 | 3,737 | [
"ASE"
] | d3e106494cb9e55ceeafd177ba521419b99ca7902926fda4d238fea513a9052c |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2000-2007 Donald N. Allingham
# Copyright (C) 2002 Gary Shao
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2009 Benny Malengier
# Copyright (C) 2009 Gary Burton
# Copyright (C) 2010 Jakim Friant
#
# This program is free... | sam-m888/gprime | gprime/plug/docgen/graphicstyle.py | Python | gpl-2.0 | 4,906 | [
"Brian"
] | eff23ff405ddf31b1f60b0d448a14d700e106791a9ee137a966b60bc90be91ba |
# -*- coding: utf-8 -*-
import os
import csv
import unittest
import pytest
from sqlalchemy.orm import Session, session
from skosprovider_sqlalchemy.models import Base, Initialiser
from skosprovider_sqlalchemy.utils import (
import_provider,
VisitationCalculator
)
from tests import DBTestCase
def _get_men... | koenedaele/skosprovider_sqlalchemy | tests/test_utils.py | Python | mit | 18,760 | [
"VisIt"
] | a63446ac7dd90f554cc87707757b835f59d09eb91346929526f5259c71935566 |
from collections import namedtuple, defaultdict
import copy
from functools import total_ordering
from itertools import izip_longest
import os
from os.path import commonprefix
import re
import urllib
from eulxml.xmlmap import StringField, XmlObject, IntegerField, NodeListField, NodeField, load_xmlobject_from_string
fro... | puttarajubr/commcare-hq | corehq/apps/app_manager/suite_xml.py | Python | bsd-3-clause | 89,116 | [
"VisIt"
] | c3ba77ad5aa8559de3f19f7ec2512b744930b346c066ef6c0387d7181a5e3b9a |
# remove VERTICES section from a VTK file
# Forrest Sheng Bao http://fsbao.net
# GNU GPL v3.0 or later
def remove(inputvtk,outputvtk):
"""Scan the inputvtk file line by line until the keyword VERTICES is found and remove corresponding lines
"""
fout=open(outputvtk, 'w')
with open(inputvtk,'r') as fin:
skip_line... | binarybottle/mindboggle_sidelined | remove_vertices.py | Python | apache-2.0 | 694 | [
"VTK"
] | cfd5e952b099e029c06bec011c35c93d39b7f7bb14751544e7d8bb75567e2fc4 |
#
# gPrime - A web-based genealogy program
#
# Copyright (C) 2007 Brian G. Matherly
# Copyright (C) 2010 Jakim Friant
# Copyright (C) 2011 Tim G L Lyons
#
# 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 Soft... | sam-m888/gprime | gprime/plug/report/_bibliography.py | Python | gpl-2.0 | 11,010 | [
"Brian"
] | 4714b76eb2d2e00e0f3e6165a7fa727f62f132b1d79ae39b19b566b2f8231d7f |
"""
Acceptance tests for Studio's Setting pages
"""
from flaky import flaky
from .base_studio_test import StudioCourseTest
from ...pages.studio.settings_certificates import CertificatesPage
class CertificatesTest(StudioCourseTest):
"""
Tests for settings/certificates Page.
"""
def setUp(self): # pyli... | Shrhawk/edx-platform | common/test/acceptance/tests/studio/test_studio_settings_certificates.py | Python | agpl-3.0 | 8,447 | [
"VisIt"
] | 202298a7df2afc8acb89cee92920b49b6041ca4fcf4fd0b1d048aced7200841e |
# -*- coding: utf-8 -*-
"""So much practical programming involves string manipulation, which
Python readily accomodates. Still, there are dozens of basic and
common capabilities missing from the standard library, several of them
provided by ``strutils``.
"""
from __future__ import print_function
import re
import sys
... | zeroSteiner/boltons | boltons/strutils.py | Python | bsd-3-clause | 32,988 | [
"MOOSE",
"Octopus"
] | 1cd8d418e95219d8d3ac34a15eb50eccbd7eaf6c0d1a79986c6e8095cd1a1da0 |
import collect_array as ca
import collect_device as cd
import collect_gen as cg
import collect_id as ci
from processing import collect_loop as cl
def print_dict_sorted(mydict):
keys = sorted(mydict)
entries = ""
for key in keys:
value = mydict[key]
entries += "'" + key + "': " + value.__... | dikujepsen/OpenTran | v2.0/framework/unused/collect_transformation_info_unused.py | Python | mit | 5,686 | [
"VisIt"
] | 0af9fc50bd421e0ce04c7d805c88c569ced5d81a2808723341e1727aea1df8ad |
# Copyright 2017 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... | jhseu/tensorflow | tensorflow/python/autograph/converters/return_statements.py | Python | apache-2.0 | 12,595 | [
"VisIt"
] | b21b12d8f438c2cd3e2c553daafe4c3ddb9741cef07c66d676e8419e0a8c313e |
# -*- coding: utf-8 -*-
#
# hl_api_simulation.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 Licen... | stinebuu/nest-simulator | pynest/nest/lib/hl_api_simulation.py | Python | gpl-2.0 | 11,956 | [
"NEURON"
] | dbd1b6199556bf52c113d648e1b7a2f622aac0a493c83fce7e0b2253baf27a3c |
#
# Copyright (C) 2013-2019 The ESPResSo project
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later... | fweik/espresso | testsuite/python/collision_detection.py | Python | gpl-3.0 | 30,592 | [
"ESPResSo"
] | a992735212d6748128c1494739ec2f3d9728ee21e9377fdb07f05d850c19d655 |
# This file is part of Merlin.
# Merlin is the Copyright (C)2008,2009,2010 of Robin K. Hansen, Elliot Rosemarine, Andreas Jacobsen.
# Individual portions may be copyright by individual contributors, and
# are included in this collective work with permission of the copyright
# owners.
# This program is free software; ... | ellonweb/merlin | Hooks/victim/topcunts.py | Python | gpl-2.0 | 4,678 | [
"Galaxy"
] | 3751c80392433038a0b39c01c4cc0675ecc30a04f23c70a687fd57f52982b0ea |
# -*- coding: utf-8 -*-
"""
Unit tests for instructor.api methods.
"""
import datetime
import ddt
import random
import pytz
import io
import json
import requests
import shutil
import tempfile
from urllib import quote
from django.conf import settings
from django.contrib.auth.models import User
from django.core import m... | nagyistoce/edx-platform | lms/djangoapps/instructor/tests/test_api.py | Python | agpl-3.0 | 193,070 | [
"VisIt"
] | 66bb00d81770a1f02444d89cba5aff4f03b38acb35c4884dbba148a5ca6c687a |
# -*- coding: utf-8 -*-
"""Deletion functions to supplement :mod:`pybel.struct.mutation.expansion`."""
import logging
import typing
from collections import Counter, defaultdict
from typing import Collection, Iterable, Optional, Tuple
import pybel.struct.mutation.expansion.neighborhood
from pybel import BELGraph
from... | pybel/pybel-tools | src/pybel_tools/mutation/expansion.py | Python | mit | 11,457 | [
"Pybel"
] | 8dce8bbe893b6b51cd17e37f251de608568951923ec44c87d47c60725529661d |
# encoding: utf-8
# Copyright (c) 2001-2016, Canal TP and/or its affiliates. All rights reserved.
#
# This file is part of Navitia,
# the software to build cool stuff with public transport.
#
# Hope you'll enjoy and contribute to this project,
# powered by Canal TP (www.canaltp.fr).
# Help us simplify mobility... | xlqian/navitia | source/jormungandr/jormungandr/realtime_schedule/siri.py | Python | agpl-3.0 | 14,796 | [
"VisIt"
] | 11bcc850bacd5d127ff04fd3dc30db4c90c56b22216e269fbe68aed6def36ac9 |
"""
Implementations of Restricted Boltzmann Machines and associated sampling
strategies.
"""
# Standard library imports
import logging
# Third-party imports
import numpy
N = numpy
np = numpy
from theano.compat import six
from theano.compat.six.moves import xrange
import theano
from theano import tensor
from theano.com... | JazzeYoung/VeryDeepAutoEncoder | pylearn2/pylearn2/models/rbm.py | Python | bsd-3-clause | 58,469 | [
"Gaussian"
] | b9824f781f382d08f9c7f21216c8c9a0518064fe1fc60613304133bff8889fae |
# coding=utf-8
from __future__ import division
import codecs
import os
import platform
import re
from .analysisperiod import AnalysisPeriod
from .designday import ASHRAEClearSky
from .designday import ASHRAETau
from .designday import DesignDay
from .designday import DryBulbCondition
from .designday import HumidityCon... | ladybug-analysis-tools/ladybug-core | ladybug/stat.py | Python | gpl-3.0 | 31,851 | [
"EPW"
] | 569c8bf340894a97d73df645d74a0f44f3adf5a7f41108085aa857f519e54be7 |
# bs.po
val = {"" : "Project-Id-Version: sheltermanager\nReport-Msgid-Bugs-To: FULL NAME <EMAIL@ADDRESS>\nPOT-Creation-Date: 2013-01-24 10:55+0000\nPO-Revision-Date: 2012-06-23 14:23+0000\nLast-Translator: Nevena <snevenas@gmail.com>\nLanguage-Team: Bosnian <bs@li.org>\nMIME-Version: 1.0\nContent-Type: text/plain; cha... | aubzen/sheltermanager | src/locale/locale_bs.py | Python | gpl-3.0 | 92,062 | [
"Amber",
"VisIt"
] | 2c1db226f68d8b2b9fa501b876f267625dfedb7ed07d9db56539aa9cbbed0391 |
#!/usr/bin/env python
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals
import sys
from tabulate import tabulate
from pymatgen import Structure
from pymatgen.symmetry.analyzer import SpacegroupAnalyzer
from... | johnson1228/pymatgen | pymatgen/cli/pmg_structure.py | Python | mit | 3,397 | [
"VASP",
"pymatgen"
] | f9d32fa97fca00fc4c01dff999d80a091625c3d3a27096d50abd2056203c6fda |
from setuptools import setup
setup(
name='pynnotator',
version='2.0',
description='A Python Annotation Framework for VCFs using multiple tools (Ex. VEP, SnpEff and SnpSift) and databases (Ex. 1000genomes, dbSNP and dbnfsp) .',
url='http://github.com/raonyguimaraes/pynnotator',
author='Rao... | raonyguimaraes/pynnotator | setup.py | Python | bsd-3-clause | 2,215 | [
"pysam"
] | 5217573d1d16b30d39b422400b289da96c1800b42ac45ae68dcd03fb578f4d94 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
from preggy import expect
from octopus import TornadoOctopus
from octopus.limiter.redis.per_domain import Limiter as PerDomainRedisLimiter
from octopus.limiter.in_memory.per_domain import Limiter as PerDomainInMemoryLimiter
from tests import TestCase
class TestTornadoCo... | heynemann/octopus | tests/test_tornado_octopus_limited.py | Python | mit | 2,319 | [
"Octopus"
] | bf50a76dd02679bac3316102bccc3ac1599dc6638156292c81d28a984a1b2681 |
import constants as c
import matplotlib
matplotlib.use('TkAgg')
import matplotlib.pyplot as plt
import numpy
import os
import qcio
import qcplot
import qcutils
import statsmodels.api as sm
import sys
import time
nfig = 0
plotwidth = 10.9
plotheight = 7.5
# load the control file
cf = qcio.load_controlfile(path='../cont... | OzFlux/OzFluxQC | scripts/compare_ah.py | Python | gpl-3.0 | 12,363 | [
"NetCDF"
] | d306f11e4829b3bf7c39b318d5c7407c214448b7631332b6cda3d9c673d13396 |
#
# Copyright (C) 2013-2018 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/wang_landau_reaction_ensemble.py | Python | gpl-3.0 | 5,481 | [
"ESPResSo"
] | 86bc7b7fe274a8300f8385fb61a3f3de43eb50d9fef7f1220239d9b26edc8366 |
# # Automatically adapted for numpy.oldnumeric Jun 27, 2008 by -c
# $Id$
#
# 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, fou... | greglandrum/rdkit | rdkit/Chem/EState/Fingerprinter.py | Python | bsd-3-clause | 2,137 | [
"RDKit"
] | 043e3de69d8d70b3352161133f6d1a17a35806ca47a3eac360ed9a8fd6cbc448 |
# Databricks notebook source
# MAGIC %md
# MAGIC ScaDaMaLe Course [site](https://lamastex.github.io/scalable-data-science/sds/3/x/) and [book](https://lamastex.github.io/ScaDaMaLe/index.html)
# MAGIC
# MAGIC This is a 2019-2021 augmentation and update of [Adam Breindel](https://www.linkedin.com/in/adbreind)'s initial ... | lamastex/scalable-data-science | dbcArchives/2021/000_6-sds-3-x-dl/056_DLbyABr_04a-Hands-On-MNIST-MLP.py | Python | unlicense | 7,004 | [
"NEURON"
] | bdf0ed423c8a2590983dfca3307d41422d9f2f013efa729f5f4d2dcf34ae2326 |
""" Schemas for structural stacks. """
import datajoint as dj
from datajoint.jobs import key_hash
import matplotlib.pyplot as plt
import numpy as np
import scanreader
from scipy import signal
from scipy import ndimage
from scipy import optimize
import itertools
from . import experiment, notify, shared, reso, meso
anat... | olakiril/pipeline | python/pipeline/stack.py | Python | lgpl-3.0 | 136,839 | [
"Gaussian"
] | 2ab1f6914b8c6b9081d5ee0e669994f6a5821e40a79fce1146585e59c7a83048 |
from PyQt5 import QtCore
from PyQt5 import QtGui
from PyQt5 import QtWidgets
import sas.qtgui.Utilities.GuiUtils as GuiUtils
class ModelViewDelegate(QtWidgets.QStyledItemDelegate):
"""
Custom delegate for appearance and behavior control of the model view
"""
def __init__(self, parent=None):
""... | SasView/sasview | src/sas/qtgui/Perspectives/Fitting/ViewDelegate.py | Python | bsd-3-clause | 11,111 | [
"Gaussian"
] | d40b78b02143369bd093822639fcb692c48f6e850fdcbd6414ecac3faa0730e4 |
# This file is part of OpenHatch.
# Copyright (C) 2010 Parker Phinney
# Copyright (C) 2009, 2010 OpenHatch, Inc.
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as published by
# the Free Software Foundation, either version 3 of the ... | mzdaniel/oh-mainline | mysite/project/tests.py | Python | agpl-3.0 | 17,510 | [
"VisIt"
] | 29bec4233a14b0484e520e5299b0c2bb432efedf07e1d04ebbe44d2d60117f82 |
# -*- coding: utf-8 -*-
#
# spike_analysis.py
#
# This file is part of NEST.
#
# Copyright (C) 2004 The NEST Initiative
#
# NEST is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 2 of the License,... | sanjayankur31/nest-simulator | examples/nest/Potjans_2014/spike_analysis.py | Python | gpl-2.0 | 6,449 | [
"NEURON"
] | e11a0a1379df3020ab305782d06b7338a54cb02bf90a50825a9ca6b537ebf74d |
# -*- coding: utf-8 -*-
#
# test_erfc_neuron.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 Licens... | lekshmideepu/nest-simulator | testsuite/pytests/test_erfc_neuron.py | Python | gpl-2.0 | 4,456 | [
"NEURON"
] | ba51c4fa70f2dc45bd9fe7e53dabac8ad3135b3c8d7e73e33cac7bf709f3ca64 |
# coding: utf-8
from __future__ import unicode_literals
from .common import InfoExtractor
import json
import random
import re
from ..compat import (
compat_parse_qs,
compat_str,
)
from ..utils import (
js_to_json,
strip_jsonp,
urlencode_postdata,
)
class WeiboIE(InfoExtractor):
_VALID_URL =... | vinegret/youtube-dl | youtube_dl/extractor/weibo.py | Python | unlicense | 4,493 | [
"VisIt"
] | 118ae5ae56f5b06ac111887c0af2f424593e15477409989441a7ae9c3ffd2afb |
"""
Photometric Redshifts via Linear Regression
-------------------------------------------
Linear Regression for photometric redshifts
We could use sklearn.linear_model.LinearRegression, but to be more
transparent, we'll do it by hand using linear algebra.
"""
# Author: Jake VanderPlas
# License: BSD
# The figure p... | nhuntwalker/astroML | book_figures/chapter9/fig_photoz_basic.py | Python | bsd-2-clause | 5,824 | [
"Gaussian"
] | 1c8bab5b0efd930a355da2366d123fbe6f5122280d5ed9a75b3e6da82732e8b7 |
from behave import *
from time import time, sleep
from selenium.common.exceptions import NoSuchElementException, WebDriverException, StaleElementReferenceException
from selenium.webdriver import ActionChains
try:
from mist.io.tests.settings import LOCAL
except ImportError:
LOCAL = True
pass
def i_am_in_h... | DimensionDataCBUSydney/mist.io | src/mist/io/tests/gui/features/steps/general.py | Python | agpl-3.0 | 12,769 | [
"VisIt"
] | 43413d17e587fec475761472a2be42c9707d4c352dfdb1160c05e117396e2003 |
# Copyright 2017 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... | asimshankar/tensorflow | tensorflow/python/data/experimental/kernel_tests/sql_dataset_test_base.py | Python | apache-2.0 | 4,471 | [
"MOE"
] | 3456ee54dba1b53f5439201331184d06555d6fcd01e893fa4ab70cc5c1747870 |
#
# Gramps - a GTK+/GNOME based genealogy program
#
# Copyright (C) 2002-2007 Donald N. Allingham
# Copyright (C) 2007-2008 Brian G. Matherly
#
# 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; ... | Forage/Gramps | gramps/gen/filters/rules/person/_hasnameof.py | Python | gpl-2.0 | 7,623 | [
"Brian"
] | b7a84ca1ee2e2caa503b2691241c9d1733844bc4a028bd236cac087170f4de0b |
# Copyright 2014 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or ... | GirlsCodePy/girlscode-coursebuilder | modules/notifications/cron.py | Python | gpl-3.0 | 6,414 | [
"VisIt"
] | 95ddc244ba53a50b06756e5963ed6365004858c227b2cde70e87a580041e362c |
# 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... | apache/climate | obs4MIPs/factory/equations.py | Python | apache-2.0 | 2,555 | [
"NetCDF"
] | 0fa172e2ad3f4a88fa08dcddf72cd5949595c84af4359af31da5b131f32d5bc2 |
##
# Copyright 2012-2016 Ghent University
#
# This file is part of EasyBuild,
# originally created by the HPC team of Ghent University (http://ugent.be/hpc/en),
# with support of Ghent University (http://ugent.be/hpc),
# the Flemish Supercomputer Centre (VSC) (https://www.vscentrum.be),
# Flemish Research Foundation (F... | Caylo/easybuild-framework | test/framework/module_generator.py | Python | gpl-2.0 | 34,555 | [
"NetCDF"
] | bc2eb1ca7fadcf512f452a4d19da9fcea497c829bb637d7535f046186302b51b |
__all__ = ["Galaxy", "Star", "SpeculativeTrade", "HexMap", "SubsectorMap2", "StatCalculation"] | makhidkarun/traveller_pyroute | PyRoute/__init__.py | Python | mit | 95 | [
"Galaxy"
] | 9fbccabe42792e0f10fcef71c3b5b3e58de4ddcc0439dba25db47c6a1b26e8d1 |
#!/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... | tszym/ansible | lib/ansible/modules/network/avi/avi_cloudconnectoruser.py | Python | gpl-3.0 | 3,676 | [
"VisIt"
] | 428ae1d324b0408d00b33057b4cfe5c524c893f184dd6a1d61acdb9222bb0b0d |
# (C) British Crown Copyright 2014, Met Office
#
# This file is part of Iris.
#
# Iris is free software: you can redistribute it and/or modify it under
# the terms of the GNU Lesser General Public License as published by the
# Free Software Foundation, either version 3 of the License, or
# (at your option) any later ve... | scollis/iris | lib/iris/tests/unit/fileformats/netcdf/test__load_cube.py | Python | gpl-3.0 | 4,057 | [
"NetCDF"
] | 198dd7408748374eba2b733471fb1d61e383f6d78dd50b4d1536840adbcd52ec |
# -*- coding: utf-8 -*-
# Copyright 2017 by Rob Gilmore and Shaurita Hutchins. All rights reserved.
# Based on ClustalOmega wrapper copyright 2011 by Andreas Wilm.
#
# Wrapper for IQTree by Rob Gilmore (2017). http://www.iqtree.org/
# Used _ClustalOmega.py as template.
#
# This code is part of the Biopython dis... | datasnakes/Datasnakes-Scripts | OrthoEvol/Orthologs/Phylogenetics/IQTree/iqtree.py | Python | mit | 6,467 | [
"Biopython"
] | 730124bd0b175f86d3218cb082f6045130eed993a4694b01aeec6279a4c282cc |
# -*- coding: utf-8 -*-
"""methods_utils.py:
Some non-standard functions generic to moose.
This library may not be exposed to end-users. Intended for development by
the maintainer of this file.
Last modified: Sat Jan 18, 2014 05:01PM
"""
__author__ = "Dilawar Singh"
__copyright__ = "... | dharmasam9/moose-core | python/moose/methods_utils.py | Python | gpl-3.0 | 1,301 | [
"MOOSE"
] | bd74becfba23e18d0880866b63c207302588e8310d39b4788d6889e531731d1f |
# -*- 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
# ... | LispyAriaro/instant-press | controllers/default.py | Python | gpl-2.0 | 21,688 | [
"VisIt"
] | 7146d5f1f71bc79d4f1cc0d0c0238b49baaa9ddbb4040ac475fc50bdd03374cf |
"""Asap utility functions
This module defines the following functions:
PrintVersion
"""
__docformat__ = "restructuredtext en"
from asap3.Internal.Builtins import _asap, get_version, get_short_version
from asap3 import __file__ as _asapfile
import ase
import sys
import os
def print_version(level = 0):
"""Print ... | auag92/n2dm | Asap-3.8.4/Python/asap3/Internal/UtilityFunctions.py | Python | mit | 3,989 | [
"ASE"
] | e10f33e93564e93356351b9fa1357ff81807e8404a58a97574102e192e645b1c |
"""This demo program solves Poisson's equation
- div C grad u(x, y) = f(x, y)
on the unit square with source f given by
f(x, y) = 10*exp(-((x - 0.5)^2 + (y - 0.5)^2) / 0.02)
and boundary conditions given by
u(x, y) = 0 for x = 0 or x = 1
du/dn(x, y) = 0 for y = 0 or y = 1
The conductivity C is a sym... | MiroK/dolfin | demo/documented/tensor-weighted-poisson/python/demo_tensor-weighted-poisson.py | Python | gpl-3.0 | 3,252 | [
"VTK"
] | 81e6cf1f34756675cfcb14d29ef6f65a985616d7b62377e0c4fea74f4e07a915 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
# (c) 2013, Jeroen Hoekx <jeroen.hoekx@dsquare.be>, Alexander Bulimov <lazywolf0@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 So... | pmazurek/ansible-modules-extras | system/lvol.py | Python | gpl-3.0 | 10,210 | [
"Firefly"
] | eae97e6d8ba2c1ff86bb7b609388929f1669b252d8d589e351476e03ab66c106 |
# Copyright 2016 Pants project contributors (see CONTRIBUTORS.md).
# Licensed under the Apache License, Version 2.0 (see LICENSE).
from __future__ import annotations
import ast
import inspect
import itertools
import sys
from abc import ABC, abstractmethod
from dataclasses import dataclass
from enum import Enum
from t... | patricklaw/pants | src/python/pants/engine/rules.py | Python | apache-2.0 | 18,044 | [
"VisIt"
] | 67a41033cc0e1544b91e1b51e6b2acf7120236dba57a6d7477b4ae07655c2f32 |
"""Gaussian processes regression. """
# Authors: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
#
# License: BSD 3 clause
import warnings
from operator import itemgetter
import numpy as np
from scipy.linalg import cholesky, cho_solve, solve_triangular
from scipy.optimize import fmin_l_bfgs_b
from sklearn.base im... | herilalaina/scikit-learn | sklearn/gaussian_process/gpr.py | Python | bsd-3-clause | 20,571 | [
"Gaussian"
] | 97caaa579b3035c325d407f9c548d4f41d934b6c88ac01dea2aeab73d61ae864 |
import pytest
import smartsheet
from datetime import datetime
from dateutil.tz import *
import json
import os
import six
@pytest.fixture(scope="module")
def smart_setup(request):
# set up a test session folder with basic starting points
smart = smartsheet.Smartsheet(max_retry_time=60)
now = datetime.now(t... | smartsheet-platform/smartsheet-python-sdk | tests/integration/conftest.py | Python | apache-2.0 | 5,275 | [
"MOE"
] | f18c6e7df63c84e67536d53b9b0f79f87ea2e7070287124891eb7120ee8eac3d |
# 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.
"""
Test the io/__init__.py module.
"""
# import iris tests first so that some things can be initialised before importing any... | rcomer/iris | lib/iris/tests/test_io_init.py | Python | lgpl-3.0 | 5,202 | [
"NetCDF"
] | ccaca962fb40272d93ad3fec57303f7fe222221d350924f2e1e48ef1ed2af69a |
# -*- coding: utf-8 -*-
# HORTON: Helpful Open-source Research TOol for N-fermion systems.
# Copyright (C) 2011-2017 The HORTON Development Team
#
# This file is part of HORTON.
#
# HORTON is free software; you can redistribute it and/or
# modify it under the terms of the GNU General Public License
# as published by th... | theochem/horton | horton/io/cp2k.py | Python | gpl-3.0 | 14,579 | [
"CP2K",
"Gaussian"
] | adf404e440a33bd9191e414f8377209391769f3d34694ac8049230dd8943d7fe |
"""Algorithms for spectral clustering"""
# Author: Gael Varoquaux gael.varoquaux@normalesup.org
# Brian Cheung
# Wei LI <kuantkid@gmail.com>
# License: BSD
import warnings
import numpy as np
from ..base import BaseEstimator, ClusterMixin
from ..utils import check_random_state, as_float_array
from ..u... | mrshu/scikit-learn | sklearn/cluster/spectral.py | Python | bsd-3-clause | 17,408 | [
"Brian",
"Gaussian"
] | a3564d66c8f1468a5cfb60a5454f86d89e3f0175e6b4bba35b57952bcb9a3a02 |
import unittest
import datetime
import json
from mock import MagicMock
from DIRAC.DataManagementSystem.Agent.RequestOperations.ReplicateAndRegister import ReplicateAndRegister
from DIRAC.RequestManagementSystem.Client.File import File
class ReqOpsTestCase( unittest.TestCase ):
""" Base class for the clients test ca... | vmendez/DIRAC | DataManagementSystem/Agent/RequestOperations/test/test_RequestOperations.py | Python | gpl-3.0 | 3,274 | [
"DIRAC"
] | 69653d5e64d34069f9cc126586b02c79b1e41c6fa3743839a7206e54da8b4f17 |
# -*- coding: utf-8 -*-
"""
Created on Thu Mar 2 14:48:24 2017
@author: thomas
"""
#from layers import Latent_Layer
import sys
import os.path
sys.path.append(os.path.abspath(os.path.join(os.path.dirname(__file__), "..")))
sys.path.append(os.path.abspath(os.path.dirname(__file__)))
import tensorflow as tf
import tens... | tmoer/multimodal_varinf | networks/toy_vae.py | Python | mit | 5,171 | [
"Gaussian"
] | 6df7b782d9445eeee7e0d6a07a2512494d753a5c81e41009cf7833d9ec63cbba |
import numpy as np
import matplotlib.pyplot as plt
from scipy.interpolate import interp1d
import PHOENIX_tools as pt
from fft_interpolate import gauss_taper
from scipy.signal import resample, hann, kaiser, boxcar
from scipy.special import i0, iv
from scipy.integrate import trapz
from numpy.fft import fft, ifft, fftfreq... | BrownDwarf/Starfish | attic/lanczos_interp.py | Python | bsd-3-clause | 12,431 | [
"Gaussian"
] | 1415034973d7bf46b1e30fc0f4ece3d482f709686d252157ad30a2fe50ec3d76 |
""" StratusLabClient
Detailed implementation of the StratusLab methods for the StratusLabClient
class. Uses the Libcloud API to connect to the StratusLab services.
Author: Charles Loomis
"""
import os
import tempfile
from ConfigParser import SafeConfigParser
from StringIO import StringIO
from conte... | myco/VMDIRAC | WorkloadManagementSystem/Client/StratusLabClient.py | Python | gpl-3.0 | 8,891 | [
"DIRAC"
] | e8c1e76ff2b68a2fc0c382de6f002ece6a8fca81023900820eeee2459bd4ea29 |
# Copyright (c) 2012 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.
"""Provides an interface to communicate with the device via the adb command.
Assumes adb binary is currently on system path.
"""
import collections
imp... | timopulkkinen/BubbleFish | build/android/pylib/android_commands.py | Python | bsd-3-clause | 47,266 | [
"Galaxy"
] | ffe387c29d6bddbf916e29ad926e32d84c461dc3286ae40e7438688ff9e1f552 |
# -*- coding: utf-8 -*-
"""
codegen
~~~~~~~
Extension to ast that allow ast -> python code generation.
:copyright: Copyright 2008 by Armin Ronacher.
:license: BSD.
"""
from ast import *
def to_source(node, indent_with=' ' * 4, add_line_information=False):
"""This function can convert a node ... | laanwj/ast_pickler | codegen.py | Python | mit | 15,495 | [
"VisIt"
] | fadc2c2ed032ffc7e5282d784a6dcc6a51fcf838fa952b2bd662e1665baea1f7 |
# ----------------------------------------------------------------------------
# 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.
# --------------------------------------------... | SamStudio8/scikit-bio | skbio/stats/ordination/_utils.py | Python | bsd-3-clause | 7,224 | [
"scikit-bio"
] | 79819ce085d618603aac685f8946c6086390b5df444700d9e73af62ba51f15e1 |
import argparse
import numpy as np
import pandas as pd
import pyproj
from netCDF4 import Dataset
from make_proj_grids import read_ncar_map_file, make_proj_grids
def main():
parser = argparse.ArgumentParser()
parser.add_argument("-s", "--start_date", required=True, help="Start date in YYYY-MM-DD format")
... | djgagne/hagelslag | hagelslag/util/lsr_calibration_dataset.py | Python | mit | 6,723 | [
"NetCDF"
] | ebc482acaa4b7781c8db027847ae2d126f717f0e90881472f6369becab20a2a1 |
import sys
from numpy import linspace, zeros, sin, exp, random, sqrt, pi, sign
from scipy.optimize import leastsq
from lmfit import Parameters, Minimizer, report_fit
from lmfit.lineshapes import gaussian
try:
import pylab
HASPYLAB = True
except ImportError:
HASPYLAB = False
HASPYLAB = False
def residual... | DiamondLightSource/auto_tomo_calibration-experimental | old_code_scripts/simulate_data/lmfit-py/examples/example_covar.py | Python | apache-2.0 | 2,319 | [
"Gaussian"
] | e2c862943ea1ac1836eec9f166aaea0c49c1e74b7d13b3e0918a0989039043c3 |
# -*- mode: python; coding: utf-8 -*-
# Copyright (c) 2018 Radio Astronomy Software Group
# Licensed under the 2-clause BSD License
"""Tests for FHD_cal object."""
import pytest
import os
import numpy as np
from pyuvdata import UVCal
import pyuvdata.tests as uvtest
from pyuvdata.data import DATA_PATH
# set up FHD f... | HERA-Team/pyuvdata | pyuvdata/uvcal/tests/test_fhd_cal.py | Python | bsd-2-clause | 13,088 | [
"Galaxy"
] | a516343a04405ee0e93947727ff7e5e7ae97ca1ed1f1a2779f3fc9d110f1a33a |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
##... | SKIRT/PTS | modeling/show/component.py | Python | agpl-3.0 | 1,503 | [
"Galaxy"
] | 30f52e61d6f4bfd9ac185b704b4d92f0406e84fc8025fab2de825d5f7519ccca |
"""
Utility functions for transcripts.
++++++++++++++++++++++++++++++++++
"""
import copy
import logging
import os
from functools import wraps
import requests
import simplejson as json
import six
from django.conf import settings
from lxml import etree
from opaque_keys.edx.locator import BundleDefinitionLocator
from ... | appsembler/edx-platform | common/lib/xmodule/xmodule/video_module/transcripts_utils.py | Python | agpl-3.0 | 40,929 | [
"FEFF"
] | 0d41698fc7beaf13c96417ea925f8ac9e14c46b7101560ab111b7017eb6da82c |
if __name__ == "__main__":
import sys,os
selfname = sys.argv[0]
full_path = os.path.abspath(selfname)[:]
last_slash = full_path.rfind('/')
dirpath = full_path[:last_slash] + '/..'
print "Append to PYTHONPATH: %s" % (dirpath)
sys.path.append(dirpath)
import time,re,logging,os
import math
imp... | mtthwflst/terse | Parsers/FchkGaussian.py | Python | mit | 13,516 | [
"Gaussian"
] | a2e6652c3203f8496383a3cbb1ceaab37e3b6a3fe457b70c3e9cda09f798d7e2 |
# Copyright (C) 2003 CAMP
# Please see the accompanying LICENSE file for further information.
"""Main gpaw module."""
import os
import sys
try:
from distutils.util import get_platform
except ImportError:
modulepath = os.environ.get('GPAW_GET_PLATFORM')
if modulepath is None:
errmsg = ('Error: Cou... | robwarm/gpaw-symm | gpaw/__init__.py | Python | gpl-3.0 | 10,531 | [
"GPAW"
] | 92948830100804ee1bc5992c4f0a4b44a1abb901c08e57b83ae80d4940e7aa86 |
# Python code to reading an image using OpenCV
import numpy as np
import cv2
import os
# Init video capture
cap = cv2.VideoCapture(0)
if cap is None or not cap.isOpened():
print('Error: unable to open video source: ', source)
exit(0)
while True:
# Capture frame-by-framehttps://github.com/iproduct/cours... | iproduct/course-social-robotics | 09-image-recognition-opencv-dnn/cv2_camera_tresholding.py | Python | gpl-2.0 | 2,292 | [
"Gaussian"
] | 7a9baeaa8ddfbf0dc97a5335b3326fae49fd9678f46569848e342eedcd5c194d |
import numpy as np
from ase import io, Atoms
def convertNames(inFile, outFile):
xyz = open(outFile,'w')
with open(inFile) as f:
for line in f:
split = line.strip().split()
if len(split) < 4:
xyz.write(line)
continue
name = split[0]
... | patrickmelix/Python4ChemistryTools | geometryAnalyzer.py | Python | mit | 7,994 | [
"ASE"
] | cc2f4366f25d8253e9e3face139e9cba7a61b489a99c1b5a2201276ad2c41801 |
#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Input file writer for SPECFEM3D_CARTESIAN.
:copyright:
Emanuele Casarotti (emanuele.casarotti@ingv.it), 2013
Lion Krischer (krischer@geophysik.uni-muenchen.de), 2013
:license:
GNU General Public License, Version 3
(http://www.gnu.org/copyleft/gpl.html)
... | KNMI/VERCE | scigateway-api/src/scigateway_services/wfs_input_generator/backends/write_SPECFEM3D_CARTESIAN_202_DEV.py | Python | mit | 7,881 | [
"VTK"
] | 9ab76eac8d57cf31c2f64c51a58f9b5966dcd6676af64f0db5f6cea6a944383e |
from distutils.core import setup
setup(
name = 'SymGP',
packages = ['SymGP'], # this must be the same as the name above
version = '0.0.1',
description = 'A symbolic algebra library for multivariate Gaussian and Gaussian process probabilistic models',
author = 'Joshua Aduol',
author_email = 'jaduol@yahoo.co.... | jna29/SymGP | symgp/setup.py | Python | mit | 529 | [
"Gaussian"
] | c134267a643d84855e39a5789f645f8cb2b42717cec35f36f436da7b9bc21741 |
# The MIT License
#
# Copyright (c) 2008
# Shibzoukhov Zaur Moukhadinovich
# szport@gmail.com
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitati... | intellimath/pyon | dumpcache.py | Python | mit | 5,027 | [
"VisIt"
] | 25004a2eb35f9c2607c70b580ed4791734f0a134ff843dcb4692390793eb1c69 |
#!/usr/bin/env python
#
# Author: Mike McKerns (mmckerns @caltech and @uqfoundation)
# Copyright (c) 1997-2015 California Institute of Technology.
# License: 3-clause BSD. The full license text is available at:
# - http://trac.mystic.cacr.caltech.edu/project/mystic/browser/mystic/LICENSE
"""
Classes for discrete meas... | jcfr/mystic | _math/discrete.py | Python | bsd-3-clause | 50,522 | [
"DIRAC"
] | 5a674cf50e348364cc9c01523b0e3a2e1e31164d21c196bd67ae7cb2d039c8f9 |
#!/usr/bin/env python
##################################################
## DEPENDENCIES
import sys
import os
import os.path
try:
import builtins as builtin
except ImportError:
import __builtin__ as builtin
from os.path import getmtime, exists
import time
import types
from Cheetah.Version import MinCompatib... | MOA-2011/enigma2-plugin-extensions-openwebif | plugin/controllers/views/mobile/channelinfo.py | Python | gpl-2.0 | 12,244 | [
"VisIt"
] | e0b4a73f016d47c4934e84dd7f9e32311891af979aa45e1e5e61f39c3cb069b9 |
# -*- coding: utf-8 -*-
"""Implements indexer for building Tophat references."""
# pylint: disable=wildcard-import,redefined-builtin,unused-wildcard-import
from __future__ import absolute_import, division, print_function
from builtins import *
# pylint: enable=wildcard-import,redefined-builtin,unused-wildcard-import
... | NKI-CCB/imfusion | src/imfusion/build/indexers/tophat.py | Python | mit | 2,753 | [
"Bowtie"
] | 8ddce046ea3c058828051856b44f435aca221072d093b049238dea188d414519 |
#!/usr/bin/env python
'''
User defined XC functional
See also
* The parser parse_xc function implemented in pyscf.dft.libxc
* Example 24-define_xc_functional.py to input a functional which is not
provided in Libxc or XcFun library.
'''
from pyscf import gto
from pyscf import dft
mol = gto.M(
atom = '''
O ... | gkc1000/pyscf | examples/dft/24-custom_xc_functional.py | Python | apache-2.0 | 5,057 | [
"PySCF"
] | a4421dd194d26fa50ee82b80503f12a58c6d26a7cf348b56d0d4ae593c13b5c1 |
#!/usr/bin/python
# -*- coding: utf-8
import argparse
from textwrap import dedent
from uuid import uuid4 as uuid
from collections import deque
from ruffus import *
import subprocess
from threading import Thread
from optparse import OptionParser
import multiprocessing
from math import frexp
import os, sys
... | Vmakarova/parallelblast | parallelblast.py | Python | apache-2.0 | 13,561 | [
"BLAST"
] | ffe6cc64c2b4d648aadd641ee560fc1c7aefb95c0255a610bf50eba90db3f9dd |
# 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 Fasta(MakefilePackage):
"""The FASTA programs find regions of local or global similarity
... | rspavel/spack | var/spack/repos/builtin/packages/fasta/package.py | Python | lgpl-2.1 | 2,127 | [
"BLAST"
] | 46b4df18156eb7f9457f5337d73f09985ff3efff05af44be806f133bcd95fa13 |
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