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import unittest2
import datetime
from google.appengine.api import urlfetch
from google.appengine.ext import db
from google.appengine.ext import ndb
from google.appengine.ext import testbed
from google.appengine.ext.webapp import Response
# from controllers.datafeed_controller import UsfirstEventDetailsGet
from model... | verycumbersome/the-blue-alliance | tests/test_datafeed_controller.py | Python | mit | 1,879 | [
"COLUMBUS"
] | 13e113bede23f1f93bfb08045e631d60a0192039ada0d5da3ac27810a8922a6b |
#!/usr/bin/env python
# -*- coding: utf8 -*-
# *****************************************************************
# ** PTS -- Python Toolkit for working with SKIRT **
# ** © Astronomical Observatory, Ghent University **
# *****************************************************************
# ... | SKIRT/PTS | modeling/tests/M81/get_headers.py | Python | agpl-3.0 | 1,867 | [
"Galaxy"
] | 4ca513dfbbe302a5d4094dc24ea5a9afa4931a3666cd61f3a7509372d283e135 |
""" Kernel module
Defines basic kernel functions of the form::
funcname(x_p, x_q, par) that return a covariance matrix.
x_p is n1*d, x_q is n2*d, the result should be n1*n2
par can be a scalar, array, or list of these.
All kernels must allow x_q=None, and efficiently compute the diagonal
of K(x_p, x_p) as a (n1... | NICTA/dora | dora/regressors/gp/kernel.py | Python | apache-2.0 | 12,947 | [
"Gaussian"
] | 24c44aa5d695ef1070e6854de2acd1be70f1dbf20af53910d677cd0407e5e5a3 |
"""
The iterative sector decomposition routines.
"""
from .common import Sector, refactorize
from ..algebra import Polynomial, Product
from ..misc import powerset
import numpy as np
# ********************** primary decomposition **********************
def primary_decomposition_polynomial(polynomial, indices=None):... | mppmu/secdec | pySecDec/decomposition/iterative.py | Python | gpl-3.0 | 11,981 | [
"DIRAC"
] | 63ad6dc787f182040a9000337bf66d2bef324460a753d1f079e09fdedcd49625 |
from edc.subject.registration.models import RegisteredSubject
from edc.subject.rule_groups.classes import (RuleGroup, site_rule_groups,
Logic, RequisitionRule)
# from .models import MaternalConsent
def func_maternal_lab(visit_instance):
visit = ['1000M']
# mater... | botswana-harvard/edc-bhp074 | bhp074/apps/eit_maternal/rule_groups.py | Python | gpl-2.0 | 1,782 | [
"VisIt"
] | 3f1a089fd4a01ce900d82a3c96e60fc6f6e515d2ecb4bab300de47a123a9d81b |
import warnings
from typing import Callable, Dict, List, Optional, Union
from torch import nn, Tensor
from torchvision.ops import misc as misc_nn_ops
from torchvision.ops.feature_pyramid_network import ExtraFPNBlock, FeaturePyramidNetwork, LastLevelMaxPool
from .. import mobilenet, resnet
from .._utils import Interme... | pytorch/vision | torchvision/models/detection/backbone_utils.py | Python | bsd-3-clause | 9,593 | [
"VisIt"
] | e669f7ca5435190461a7cd4819de57f1a92d80ff96bc346aca1cbea9465c3571 |
from __future__ import print_function
from __future__ import division
from __future__ import absolute_import
import sys, os
import numpy as np
import numpy.testing as npt
import scipy.spatial.distance
from unittest import skipIf
from mdtraj.utils.six.moves import xrange
from msmbuilder import metrics
from common impo... | msmbuilder/msmbuilder-legacy | tests/test_rmsd.py | Python | gpl-2.0 | 1,970 | [
"MDTraj"
] | 0fe3e240a87bd10364ca1abf7ac09d7c08c9af0d7d38875f3572e47d10170359 |
# Hidden Markov Model Implementation
import pylab as pyl
import numpy as np
import matplotlib.pyplot as pp
#from enthought.mayavi import mlab
import scipy as scp
import scipy.ndimage as ni
import roslib; roslib.load_manifest('sandbox_tapo_darpa_m3')
import rospy
#import hrl_lib.mayavi2_util as mu
import hrl_lib.viz ... | tapomayukh/projects_in_python | classification/Classification_with_HMM/Single_Contact_Classification/area_codes/number_of_states/hmm_crossvalidation_area_15_states.py | Python | mit | 17,008 | [
"Gaussian",
"Mayavi"
] | b7db6493e38ffee9c3b0fc7e7773c203fbf863ddf63f7b6ef7aff5a2a91ad3f2 |
# -*- coding: utf-8 -*-
"""
sphinx.writers.manpage
~~~~~~~~~~~~~~~~~~~~~~
Manual page writer, extended for Sphinx custom nodes.
:copyright: Copyright 2007-2016 by the Sphinx team, see AUTHORS.
:license: BSD, see LICENSE for details.
"""
import warnings
from docutils import nodes
from docutils.wr... | bgris/ODL_bgris | lib/python3.5/site-packages/Sphinx-1.5.1-py3.5.egg/sphinx/writers/manpage.py | Python | gpl-3.0 | 13,713 | [
"VisIt"
] | 8b642afa0434e4ca7785b199177ebbaf6cff9cd4ecb8df788feb0885537d6b1c |
# -*- coding: utf-8 -*-
'''
Master Reborn Add-on
Copyright (C) 2017 Master Reborn
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later versio... | TheWardoctor/Wardoctors-repo | plugin.video.master.reborn/resources/lib/indexers/navigator.py | Python | apache-2.0 | 36,796 | [
"BLAST"
] | e6de981a75f03f186eabf540a4642f9a3e2cd89a9d541697c68537cdb140959b |
# Copyright 2016 Google Inc. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or a... | ivano666/tensorflow | tensorflow/contrib/distributions/python/ops/mvn.py | Python | apache-2.0 | 17,863 | [
"Gaussian"
] | 7820f53a56ae0b88bc502aabe5116e1589afefe30ffbfc4aa1ebf04023966d01 |
"""Functions to plot epochs data."""
# Authors: Alexandre Gramfort <alexandre.gramfort@telecom-paristech.fr>
# Denis Engemann <denis.engemann@gmail.com>
# Martin Luessi <mluessi@nmr.mgh.harvard.edu>
# Eric Larson <larson.eric.d@gmail.com>
# Jaakko Leppakangas <jaeilepp@student.jyu.f... | teonlamont/mne-python | mne/viz/epochs.py | Python | bsd-3-clause | 85,327 | [
"Gaussian"
] | 0a1127369dc7e2364cad275cbe1b3ede14916257451acaf7b9dfff939be5f748 |
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
# Molecular Dynamics Trajectories.
# Copyright 2012-2013 Stanford University and the Authors
#
# Authors: Robert McGibbon
# Contributors:
#
# MDTraj is free software: y... | dwhswenson/mdtraj | mdtraj/utils/validation.py | Python | lgpl-2.1 | 8,147 | [
"MDTraj"
] | 2c00a77111bf2f1970c6fc1d503b01a84621a663d816fcddd0ad2bf5ea49e63d |
# Copyright 2011-2013 Free Software Foundation, Inc.
#
# This file is part of GNU Radio
#
# SPDX-License-Identifier: GPL-3.0-or-later
#
#
'''
Blocks and utilities for digital modulation and demodulation.
'''
from __future__ import absolute_import
from __future__ import unicode_literals
# The presence of this file tu... | jdemel/gnuradio | gr-digital/python/digital/__init__.py | Python | gpl-3.0 | 1,248 | [
"Gaussian"
] | 78b948cd51b41fc0ae863acf0b75fbf6e719329a05af1825248087c82351eb70 |
# -*- coding: utf-8 -*-
"""
celery.datastructures
~~~~~~~~~~~~~~~~~~~~~
Custom types and data structures.
"""
from __future__ import absolute_import, print_function, unicode_literals
import sys
import time
from collections import defaultdict, Mapping, MutableMapping, MutableSet
from heapq import heappus... | hubert667/AIR | build/celery/celery/datastructures.py | Python | gpl-3.0 | 18,598 | [
"VisIt"
] | 83ba955c97537b7226685bf21d6548488ccc594b221121cd07ee65834a2462e1 |
from go_somewhere_significant import *
from go_to_adjacent_systems import *
import Briefing
import Director
import VS
import debug
import faction_ships
import launch
import quest
import unit
import universe
import vsrandom
class escort_local (Director.Mission):
def __init__(self, factionname, numsystemsaway, ene... | ermo/privateer_wcu | modules/missions/escort_local.py | Python | gpl-2.0 | 11,281 | [
"VisIt"
] | 6732c3244787bb9faab0f3af84f8da04b12e8f19ff084ffbb078a0af574693a4 |
"""
Test rdkit_grid_featurizer module.
"""
import os
import unittest
import numpy as np
import pytest
from deepchem.feat.complex_featurizers import rdkit_grid_featurizer as rgf
np.random.seed(123)
def random_string(length, chars=None):
import string
if chars is None:
chars = list(string.ascii_letters + str... | lilleswing/deepchem | deepchem/feat/tests/test_rdkit_grid_features.py | Python | mit | 23,753 | [
"RDKit"
] | 62de3aa0263176131c8f9d792b51fc8afcae81a1c06ee440b6c34659c85fd7a2 |
#!/usr/bin/env python
# Copyright 2014-2020 The PySCF Developers. All Rights Reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# U... | sunqm/pyscf | pyscf/mcscf/mc2step.py | Python | apache-2.0 | 7,056 | [
"PySCF"
] | 8d3da47b32339a5085ab4cc513b616c42c12930d633d0a8e4def1332f128183a |
# -*- coding: utf-8 -*-
#
# test_refractory.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... | tillschumann/nest-simulator | pynest/nest/tests/test_refractory.py | Python | gpl-2.0 | 8,437 | [
"NEURON"
] | d0401d0a111ce83f99980db6b619e28081ee54af3cfacd8c7d3659f218583be6 |
# 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... | allenlavoie/tensorflow | tensorflow/contrib/autograph/converters/break_statements.py | Python | apache-2.0 | 4,048 | [
"VisIt"
] | 9bce6137149eb567b583c30f6b45581ca9392928d673526f95c67e32419cfd38 |
#!/usr/bin/env python
##############################################################################################
#
#
# regrid_emissions_N96e.py
#
#
# Requirements:
# Iris 1.10, time, cf_units, numpy
#
#
# This Python script has been written by N.L. Abraham as part of the UKCA Tutorials:
# http://www.ukca.ac.u... | acsis-project/emissions | emissions/python/timeseries_1960-2020/regrid_OC_fossil_emissions_n96e_360d.py | Python | gpl-3.0 | 17,348 | [
"NetCDF"
] | 985a35997ba4312150a7ddadfa5bfc19791f763bc147ec2633048da99bf437ed |
'''
===============================================================
:mod:`gridcells.analysis.fields` - grid field related analysis
===============================================================
The :mod:`~gridcells.analysis.fields` module contains routines to analyse
spiking data either from experiments involoving a ... | lsolanka/gridcells | gridcells/analysis/fields.py | Python | gpl-3.0 | 7,043 | [
"Gaussian",
"NEURON"
] | b04fb65916d8a247e9e7370f4286fde0e7ede2f59388f1435f9232f05482b468 |
# -*- coding: utf-8 -*-
from __future__ import unicode_literals
from django.db import models, migrations
import multiselectfield.db.fields
from django.conf import settings
class Migration(migrations.Migration):
dependencies = [
('branch', '0029_auto_20141203_1434'),
]
operations = [
mig... | MaximeBiset/care4care | branch/migrations/0030_auto_20141203_1712.py | Python | agpl-3.0 | 4,193 | [
"VisIt"
] | d2a0ec7330ca5801e8635ef03e5ee6f06e7040a5fd25a2a09ee35049ad4d2396 |
# Experiment script to compare ReLU dAs versus Gaussian-Bernoulli dAs
# Train each with varying amounts of noise,
import numpy
import theano
import theano.tensor as T
from theano.tensor.shared_randomstreams import RandomStreams
from AutoEncoder import AutoEncoder
from AutoEncoder import ReluAutoEncoder
from AutoEnco... | lzamparo/SdA_reduce | theano_models/dA/ReLU_vs_GB_test_script.py | Python | bsd-3-clause | 5,659 | [
"Gaussian"
] | 1fa9d9ed63b1292f4762fdb3b9ce6539f3b53d38c1e4b1c23a398f81f50ae86b |
#!/galaxy/home/mgehrin/hiclib/bin/python
"""
Filter maf blocks for presence of wildcard columns. Blocks must meet the
criteria of having at least `min_good` columns, each of which has more than
`min_species` rows that are NOT wildcard bases ('*').
TODO: Allow specifying the character of the wildcard base.
usage: %p... | bxlab/HiFive_Paper | Scripts/HiCLib/bx-python-0.7.1/build/scripts-2.7/maf_filter_max_wc.py | Python | bsd-3-clause | 925 | [
"Galaxy"
] | 7efb71af9b75b46d789a17eb7676b9e61f66d166ce581b71e3b5126b4cbcf020 |
# 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... | apark263/tensorflow | tensorflow/python/kernel_tests/signal/spectral_ops_test.py | Python | apache-2.0 | 14,519 | [
"Gaussian"
] | 517c866a289a066e102eedc08f37b9fc8b6daf3c3ce7650c1b3383fa1c5d5af9 |
from django.test import TestCase, tag
from edc_appointment.models import Appointment
from edc_base import get_utcnow
from edc_reference import site_reference_configs
from edc_visit_schedule.site_visit_schedules import site_visit_schedules
from edc_visit_tracking.constants import SCHEDULED
from ..metadata_wrappers impo... | botswana-harvard/edc-meta-data | edc_metadata/tests/test_metadata_wrappers.py | Python | gpl-2.0 | 6,408 | [
"VisIt"
] | 1e04e9d41922383d3ff6d612c514aa01b78f9a439321792723081b1128953c70 |
# -*- coding: utf-8 -*-
# Copyright (c) 2015-2020, Exa Analytics Development Team
# Distributed under the terms of the Apache License 2.0
from unittest import TestCase
from exatomic.molcas.editor import Editor
class TestEditor(TestCase):
"""Tests that metadata is set appropriately for Molcas editors."""
def ... | exa-analytics/atomic | exatomic/molcas/tests/test_editor.py | Python | apache-2.0 | 762 | [
"MOLCAS"
] | 39c38b46599133fd0488db24c16e19506008da2505657e303dd5f34d83eb87a7 |
# coding=utf-8
"""
Tests for the course home page.
"""
from datetime import datetime, timedelta
import ddt
import mock
from django.conf import settings
from django.urls import reverse
from django.http import QueryDict
from django.utils.http import urlquote_plus
from django.utils.timezone import now
from pytz import UT... | philanthropy-u/edx-platform | openedx/features/course_experience/tests/views/test_course_home.py | Python | agpl-3.0 | 39,942 | [
"VisIt"
] | f2a5839966e46be4b638ceffeddac7f5d5429504efee96525e2da7a209ddbe08 |
# 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 | poem/pr_vipe/infer.py | Python | apache-2.0 | 9,658 | [
"Gaussian"
] | 71efe21d2c3479a30d975635de43968e30362a77da38ba0870ca798c61e5d87c |
# mako/_ast_util.py
# Copyright 2006-2021 the Mako authors and contributors <see AUTHORS file>
#
# This module is part of Mako and is released under
# the MIT License: http://www.opensource.org/licenses/mit-license.php
"""
ast
~~~
This is a stripped down version of Armin Ronacher's ast module.
:copyr... | sqlalchemy/mako | mako/_ast_util.py | Python | mit | 20,247 | [
"VisIt"
] | 9d3b3a617c7680ecd395b7903343eb363fbefafe84dede946a2f728a5975e1f2 |
r"""
This module is a VTK Web server application.
The following command line illustrate how to use it::
$ vtkpython .../vtk_web_graph.py --vertices 1000 --edges 400
Any VTK Web executable script come with a set of standard arguments that
can be overriden if need be::
--host localhost
... | berendkleinhaneveld/VTK | Web/Applications/GraphLayout/server/vtk_web_graph.py | Python | bsd-3-clause | 6,396 | [
"VTK"
] | 856be57af4e027f1adbf94251f023346bbc33896019f2b94b288292eb4405d29 |
"""
This sample demonstrates a simple skill built with the Amazon Alexa Skills Kit.
The Intent Schema, Custom Slots, and Sample Utterances for this skill, as well
as testing instructions are located at http://amzn.to/1LzFrj6
For additional samples, visit the Alexa Skills Kit Getting Started guide at
http://amzn.to/1LG... | chanyoonzhu/eatquik | eatquik.py | Python | mit | 18,563 | [
"VisIt"
] | 74fcdcc832be0af11230ad74e3adb932bfa6f14846925ac318caf613d80e1fac |
from __future__ import division, absolute_import, print_function
import os
import sys
import types
import re
import warnings
from numpy.core.numerictypes import issubclass_, issubsctype, issubdtype
from numpy.core import ndarray, ufunc, asarray
# getargspec and formatargspec were removed in Python 3.6
from numpy.com... | LumPenPacK/NetworkExtractionFromImages | win_build/nefi2_win_amd64_msvc_2015/site-packages/numpy/lib/utils.py | Python | bsd-2-clause | 34,996 | [
"VisIt"
] | 4620a3ea5b47e1966930293b530dea38fdcc8e305061677f0c52deb7fb6f940d |
import hashlib
import os
import shutil
import typing as T
import cdsapi # type: ignore
SAMPLE_DATA_FOLDER = os.path.join(os.path.dirname(__file__), "sample-data")
EXTENSIONS = {"grib": ".grib", "netcdf": ".nc"}
def ensure_data(dataset, request, folder=SAMPLE_DATA_FOLDER, name="{uuid}.grib"):
# type: (str, T.Di... | ecmwf/cfgrib | tests/cdscommon.py | Python | apache-2.0 | 914 | [
"NetCDF"
] | 2699920a8902acd703c5ef80bfbea68cfebfb77e3d96e0a02c12f127a8189efc |
# Orca
#
# Copyright 2014 Igalia, S.L.
#
# Author: Joanmarie Diggs <jdiggs@igalia.com>
#
# 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 o... | pvagner/orca | src/orca/scripts/apps/epiphany/script.py | Python | lgpl-2.1 | 1,664 | [
"ORCA"
] | e41ee22eb4db0c1210994c91cdb7ebc815ace448f4ac47581a3c0836b68bbda7 |
import json
import logging
import sys
import networkx as nx
from networkx.algorithms import weakly_connected_component_subgraphs
from collections import defaultdict
from itertools import chain, ifilter
from functools import partial
from synapseclustering import tree_max_density
from numpy import subtract
from numpy.l... | catsop/CATMAID | django/applications/catmaid/control/graph.py | Python | gpl-3.0 | 19,605 | [
"NEURON"
] | 7818c0028bf262dc1f6c90dd0bf71ec17598144f9b98744ab13cea13206b7891 |
# -*- coding: utf-8 -*-
"""
Acceptance tests for CMS Video Module.
"""
from unittest import skipIf
from ...pages.studio.auto_auth import AutoAuthPage
from ...pages.studio.overview import CourseOutlinePage
from ...pages.studio.video.video import VidoComponentPage
from ...fixtures.course import CourseFixture, XBlockFix... | LICEF/edx-platform | common/test/acceptance/tests/video/test_studio_video_module.py | Python | agpl-3.0 | 3,784 | [
"VisIt"
] | 5393f69a550781a4d3a12e0b915f88065ff4ada5e6f9e81559d0e62bacac9d51 |
# Copyright (c) Charl P. Botha, TU Delft
# All rights reserved.
# See COPYRIGHT for details.
from module_base import ModuleBase
from module_mixins import NoConfigModuleMixin
import module_utils
import vtk
import numpy
class FitEllipsoidToMask(NoConfigModuleMixin, ModuleBase):
def __init__(self, module_manager):
... | nagyistoce/devide | modules/filters/FitEllipsoidToMask.py | Python | bsd-3-clause | 5,248 | [
"VTK"
] | cc0b04124e14a6d29e158c2aab6370b657c91d9b812e01c0dcb513ef7a6d8343 |
"""Validate dependencies."""
import ast
from pathlib import Path
from typing import Dict, Set
from homeassistant.requirements import DISCOVERY_INTEGRATIONS
from .model import Integration
class ImportCollector(ast.NodeVisitor):
"""Collect all integrations referenced."""
def __init__(self, integration: Integ... | Teagan42/home-assistant | script/hassfest/dependencies.py | Python | apache-2.0 | 7,786 | [
"VisIt"
] | 57ef5e0d4e8bcc61a4e2e1eb90fc1894cb1854be1f98b73f281ef06b07a48b6a |
#!/usr/bin/env python3
# -*- coding: utf-8 -*-
#
# perses documentation build configuration file, created by
# sphinx-quickstart on Sun May 14 17:09:48 2017.
#
# This file is execfile()d with the current directory set to its
# containing dir.
#
# Note that not all possible configuration values are present in this
# aut... | choderalab/perses | docs/conf.py | Python | mit | 6,395 | [
"MDTraj",
"OpenMM"
] | 89157566599886584ca100e99eebb015292c6b49acb66abb6ea11b2db74f9d68 |
# Created by John Travers, Robert Hetland, 2007
""" Test functions for rbf module """
import numpy as np
from numpy.testing import (assert_, assert_array_almost_equal,
assert_almost_equal)
from numpy import linspace, sin, cos, random, exp, allclose
from scipy.interpolate.rbf import Rbf
FUNC... | WarrenWeckesser/scipy | scipy/interpolate/tests/test_rbf.py | Python | bsd-3-clause | 6,546 | [
"Gaussian"
] | 8c4d4bcae9bd7cbce0b60d74fc15627c40ae44aa96735414388a643fd8943b91 |
from ase import *
a = 3.6
b = a / 2
fcc = Atoms('Cu', positions=[(0, 0, 0)],
cell=[(0, b, b), (b, 0, b), (b, b, 0)],
pbc=1)
fcc *= (2, 1, 1)
fcc.set_calculator(EMT())
fcc.set_momenta([(0.9, 0.0, 0.0), (-0.9, 0, 0)])
md = VelocityVerlet(fcc, dt=0.1)
def f():
print fcc.get_potential_energy(), ... | freephys/python_ase | ase/test/md.py | Python | gpl-3.0 | 487 | [
"ASE"
] | 807b39deefc93a7239e447f4a1ddab9db56690602fbee2f5b820b1ea1fe6baaa |
# dataset.py
"""Module for Dataset class
Overview of Dicom object model:
Dataset(derived class of Python's dict class)
contains DataElement instances (DataElement is a class with tag, VR, value)
the value can be a Sequence instance
(Sequence is derived from Python's list),
or just a regular value... | mshunshin/SegNetCMR | pydicom/dataset.py | Python | mit | 42,434 | [
"VisIt"
] | 1e3fe5d58b2cfa28f62ba39115e396cc6601df03d4d0a58055830eaccd5fd22f |
"""
Example ThirdWay experimentations.
"""
from __future__ import absolute_import, print_function
import matplotlib.pyplot as plt
import numpy as np
from thirdway.lightcurve import LightCurve, generate_lc_depth, kepler17_params_db
from thirdway.fitting import peak_finder, summed_gaussians, gaussian
from astropy.utils.c... | jradavenport/ThirdWay | example_k17_bfgs.py | Python | mit | 3,447 | [
"Gaussian"
] | 47cffe1ce31d842184f0817260c8f08059adb3d9d7c7d200e864cf5cc0079ff7 |
"""Contains the classes that deal with constant temperature dynamics.
Copyright (C) 2013, Joshua More and Michele Ceriotti
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 Lic... | quang-ha/lammps | tools/i-pi/ipi/engine/thermostats.py | Python | gpl-2.0 | 34,428 | [
"Gaussian"
] | 77cecca07b6bc4bb9719b2a55775231a7c98af27da62951200b22cf7f6cffa7f |
import gzip
import pysam
import timeit
iterations = 5
repeats = 100
print ("repeats=", repeats, "iterations=", iterations)
fn_compressed = '/tmp/windows_small.bed.gz'
fn_uncompressed = '/tmp/windows_small.bed'
def test_python_compressed():
'''iterate through with python.'''
f = gzip.open( fn_compressed)
... | daler/pysam | benchmark/tabix_bench.py | Python | mit | 2,349 | [
"pysam"
] | a1ceea711394112ea296af62cded12f7e98d25c28c099c191a0403da0480fdde |
from lab02.Neuron import Neuron
class NeuralNetwork:
def __init__(self, population, size):
self.size = size
self.network = []
for i in range(size):
self.network.append(Neuron(population))
def train(self, learning_set, epoch, learning_rate):
for i in range(epoch):
... | lucekdudek/si | lab03/NauralNetwork.py | Python | apache-2.0 | 1,831 | [
"NEURON"
] | 388e1b96413e6d1e1a35617fe830ed1acc4593f49ae6f19a4325229b99240c9f |
# ============================================================================
#
# Copyright (C) 2007-2012 Conceptive Engineering bvba. All rights reserved.
# www.conceptive.be / project-camelot@conceptive.be
#
# This file is part of the Camelot Library.
#
# This file may be used under the terms of the GNU General... | jeroendierckx/Camelot | camelot/view/controls/editors/smileyeditor.py | Python | gpl-2.0 | 3,375 | [
"VisIt"
] | 6f14f1cbfe5bf1d23cf13a08446844a57016b957f1eed6bc749cbe89c487b95c |
"""
../wps.py?request=execute
&service=wps
&version=1.0.0
&identifier=esmvaltool-perfmetrics
&status=true
&storeExecuteResponse=true
"""
import datetime
import shutil
import netCDF4
import urlparse
from pywps.Process import WPSProcess
import os
import logging
from jinja2 import FileSystemLoader, Environment,select... | c3s-magic/adaguc-services-esmvaltool-wps | processes/esmvaltool-clouds.py | Python | apache-2.0 | 5,199 | [
"NetCDF"
] | 36c937b08524eb1e1fb1fb337bf56b5f2c9bb0e97d446a432a83f7c95ddda65e |
#!/usr/bin/env python
########################################################################
# $HeadURL$
########################################################################
""" Enable using one or more Storage Elements
"""
__RCSID__ = "$Id$"
import DIRAC
from DIRAC.Core.Base import Script
read = True
write = Tr... | marcelovilaca/DIRAC | DataManagementSystem/scripts/dirac-admin-allow-se.py | Python | gpl-3.0 | 8,412 | [
"DIRAC"
] | ef7c42781756c7388c657b86623ad8de9ea95b816177494aee1847e40dc358bd |
#!/usr/bin/python
# -*- coding: utf-8 -*-
"""
Script to upload images to wikipedia.
Arguments:
-keep Keep the filename as is
-filename Target filename without the namespace prefix
-noverify Do not ask for verification of the upload description if one
is given
-abortonwarn: Abor... | npdoty/pywikibot | scripts/upload.py | Python | mit | 7,699 | [
"VisIt"
] | 38ccf719c5073b79434999c433fe7119d4f4fb95bdd00460c4dfd6c36276f311 |
#!/usr/bin/env python3
# Copyright (C) 2013-2019 The ESPResSo project
# Copyright (C) 2012 Olaf Lenz
#
# This file is part of ESPResSo.
#
# ESPResSo is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either versi... | espressomd/espresso | src/config/featuredefs.py | Python | gpl-3.0 | 6,111 | [
"ESPResSo"
] | 018c7ee8168b6539baaab3e058cd626e3381ff6cab92d917a6bdf6e71b23755d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
from __future__ import division, unicode_literals, print_function
<<<<<<< HEAD
"""
Module implementing classes and functions to use Zeo++.
Zeo++ can be obtained from http://www.maciejharanczyk.info/Zeopp/
"""
... | Bismarrck/pymatgen | pymatgen/io/zeopp.py | Python | mit | 23,655 | [
"GULP",
"pymatgen"
] | 595552d7fc1b652f7b2c67ed2638174ba8857a9ad153265ec8b9a3287dd98c14 |
import copy
import logging
import mcerp
import numpy as np
import scipy.stats as ss
from mcerp import *
from utils.kde import Transformations
from utils.boxcox import BoxCox
class Distribution(object):
""" Distributional representation of uncertain variables.
"""
NON_ZERO_FACTOR = 1e-6
B_CACHE = {}
... | UCSBarchlab/Archrisk | models/distributions.py | Python | bsd-3-clause | 9,102 | [
"Gaussian"
] | 247c0bcbb2c768b7eb625e5856a0462f56a76679e548c6e3447f24dc737beff1 |
from PySide.QtGui import QColor
__author__ = 'MaitreyaBuddha'
# Light theme
BACKGROUND_LIGHT = QColor("#FAFAFA")
CARD_LIGHT = QColor("#FFFFFF")
# Dark theme
BACKGROUND_DARK = QColor("#303030")
CARD_DARK = QColor("#424242")
# Teal-Amber color palette
DARK_PRIMARY_COLOR = QColor("#00796B")
PRIMARY_COLOR = QColor("#00... | samvidmistry/PyMaterial | MUtilities/MColors.py | Python | mit | 533 | [
"Amber"
] | 6cbcd3f2b232425b0b3b69136c0a5ba0002942cd1867956e7103ad7423a16c43 |
#!/usr/bin/python
# -*- coding: utf-8 -*-
#
# Copyright: (c) 2017, F5 Networks Inc.
# GNU General Public License v3.0 (see COPYING or https://www.gnu.org/licenses/gpl-3.0.txt)
from __future__ import absolute_import, division, print_function
__metaclass__ = type
ANSIBLE_METADATA = {'metadata_version': '1.1',
... | veger/ansible | lib/ansible/modules/network/f5/_bigip_asm_policy.py | Python | gpl-3.0 | 38,818 | [
"Galaxy"
] | 6ebdba6a99097d29fac0c8c0c4619601b0d867d734dccacc428acdd469b48a4d |
from abc import ABCMeta, abstractmethod
class OpticAxisRule(object):
# return values of neighbor_for_photor and
# neighbor_that_provide_photor should be the
# following:
# [x] is the neighbor at position x
# [x, y] is the neighbor at position y
# of neighbor at position x
# this is commuta... | neurokernel/retina | retina/geometry/opticaxis.py | Python | bsd-3-clause | 9,626 | [
"NEURON"
] | 363b6556607915c87f3620324d32131d4f1966ff1847dc6e9f26e846359f663b |
from MeshInfo import *
''' Provides Information about ExodusII meshes '''
class ExodusIIMeshInfo(MeshInfo):
def __init__(self, mesh_item_data, file_name):
MeshInfo.__init__(self, mesh_item_data)
self.file_name = file_name
import vtk
reader = vtk.vtkExodusIIReader()
reader.SetFileName(self.file_na... | gleicher27/Tardigrade | moose/gui/mesh_info/ExodusIIMeshInfo.py | Python | lgpl-2.1 | 1,654 | [
"VTK"
] | d9a685d66923eece0fe6d26575b32d3a6dffc509e05bae81d2a242c3e993cad0 |
#! /usr/bin/env python
from MDAnalysis import *
import numpy
import math
import sys
my_traj = sys.argv[1]
u = Universe("init.pdb",my_traj)
v = Universe("init.pdb")
end = my_traj.find('.pdb')
fout_name = 'pepdist.dat'
# helices
a = u.selectAtoms("segid A and resid 50:73")
b = u.selectAtoms("segid B and resid 56:86"... | demharters/git_scripts | dist_pep_mhcii.py | Python | apache-2.0 | 629 | [
"MDAnalysis"
] | 1ec3a469fc089322e0438a71175f6d5facffc627aa07c2b61b60fc0939643ae9 |
"""Tests for the CheckMigration Operation"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
import functools
import pytest
from mock import MagicMock
from DIRAC import S_OK
from DIRAC.RequestManagementSystem.Client.File import File
from DIRAC.RequestManag... | yujikato/DIRAC | src/DIRAC/DataManagementSystem/Agent/RequestOperations/test/Test_CheckMigration.py | Python | gpl-3.0 | 4,209 | [
"DIRAC"
] | 1a6f54ab02d4f0403e6cd3ef94659f7e2114e9c94306f8a9ccab21f2b863eb02 |
"""
Bond order information.
"""
CCDC_BOND_ORDERS = {
# http://cima.chem.usyd.edu.au:8080/cif/skunkworks/html/ddl1/mif/bond.html
'S': 1.0, # single (two-electron) bond or sigma bond to metal
'D': 2.0, # double (four-electron) bond
'T': 3.0, # triple (six-electron) bond
'Q': 4.0, # quadruple (eigh... | peteboyd/lammps_interface | lammps_interface/ccdc.py | Python | mit | 949 | [
"CRYSTAL"
] | 08631d43443fe3932109fa97ec891ab6aebad1a0c766ae9a53eb2ab6321db688 |
import logging
import urllib2
import urllib
import re
import os
import time
from pprint import pprint
from stringcookiejar import StringCookieJar
headers = {
'User-Agent': 'Mozilla/5.0 (Windows; U; Windows NT 5.1; ru; rv:1.9.0.'
'13) Gecko/2009073022 Firefox/3.0.13 (.NET CLR 3.5.30729)',
'Acc... | trashgenerator/vkontakte-spy | vkontakte_spy/connectors.py | Python | bsd-3-clause | 6,677 | [
"VisIt"
] | d80b49b4c77d5762a496ba8401a327b3c0e16e29028c177dbb2f88b5e331bac9 |
# -*- coding: utf-8 -*-
#
# Moonstone is platform for processing of medical images (DICOM).
# Copyright (C) 2009-2011 by Neppo Tecnologia da Informação LTDA
# and Aevum Softwares LTDA
#
# This file is part of Moonstone.
#
# Moonstone is free software: you can redistribute it and/or modify
# it under the terms of the GN... | zoulianmp/moonstone-pyqt | moonstone/main.py | Python | lgpl-3.0 | 7,136 | [
"VTK"
] | eef42c86c708029a248fd7d536e4b8f7084ccc293fa044274b864e49101cd605 |
#!/usr/bin/env python
# Written by Rose A. Finn, Nov 9, 2013
#
'''
goal is to match Luc Simard's B/D GIM2D catalog with my NSA catalogs.
Simard catalog is in research/SimardSDSS2011/table1and3.fits
this has 108 columns!!!
I would like to figure out a way to do this without have to write out every column
individually... | rfinn/LCS | paper1code/LCSmatchSimardBD2NSA.py | Python | gpl-3.0 | 15,568 | [
"Galaxy"
] | 1d8163482ea9619f73a5d7731bcf2dba52911e318b716483f0b9c5d65a6cffbc |
from __future__ import print_function, division
import math
import numpy as np
def map_lattice_to_coordinate_space(grid, x, y=None):
"""Maps the lattice coordinate to the coordinate space depending on the
coordinate system.
Parameters
----------
* `grid`: Lattice object
Defines the topolo... | trotter-suzuki-mpi/trotter-suzuki-mpi | src/Python/trottersuzuki/tools.py | Python | gpl-3.0 | 7,676 | [
"Gaussian"
] | 458648a896b4b4587c8e66493dc79c187abe395ccf888a7860a2df2de84059c2 |
"""
Serializes a Cython code tree to Cython code. This is primarily useful for
debugging and testing purposes.
The output is in a strict format, no whitespace or comments from the input
is preserved (and it could not be as it is not present in the code tree).
"""
from Cython.Compiler.Visitor import TreeVisitor
from C... | JulienMcJay/eclock | windows/Python27/Lib/site-packages/Cython/CodeWriter.py | Python | gpl-2.0 | 14,900 | [
"VisIt"
] | a925b97e5d898a00155e034aec71e67f2ae9407e829bedaa62e93c2fd151c712 |
# Copyright (C) 2018
# 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, either version 3 of the License, o... | MrTheodor/espressopp | src/interaction/TabulatedSubEnsAngular.py | Python | gpl-3.0 | 5,918 | [
"ESPResSo"
] | 74624a26833a549bc9efd6422e1bece05cbe2838b5579a9bb06fea0f23081fb9 |
# -*- coding: utf-8 -*-
# vi:si:et:sw=4:sts=4:ts=4
##
## Copyright (C) 2010-2013 Async Open Source <http://www.async.com.br>
## All rights reserved
##
## This program is free software; you can redistribute it and/or modify
## it under the terms of the GNU General Public License as published by
## the Free Software Fou... | tiagocardosos/stoq | stoqlib/domain/test/test_loan.py | Python | gpl-2.0 | 16,508 | [
"VisIt"
] | d8d7fdb6acb9143d498cdd8c3e1af7b3fdba5ec4ebb140391bd6199301b5450c |
""" MQProducer
"""
from __future__ import absolute_import
from __future__ import division
from __future__ import print_function
from DIRAC import gLogger
from DIRAC.Resources.MessageQueue.Utilities import getDestinationAddress, getMQService
class MQProducer(object):
def __init__(self, mqManager, mqURI, producerI... | ic-hep/DIRAC | src/DIRAC/Resources/MessageQueue/MQProducer.py | Python | gpl-3.0 | 1,400 | [
"DIRAC"
] | cf4e7cc445d8fa998d542aa2d0f5e250484c5dc821198554c424e617e315ba50 |
# 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 main loading API.
"""
# import iris tests first so that some things can be initialised before importing anything... | SciTools/iris | lib/iris/tests/test_load.py | Python | lgpl-3.0 | 6,632 | [
"NetCDF"
] | aba0b7d227091f4fbf438d430c6fdf74ee4a47b42c9e14ba66a1f5c9ab7aa261 |
#!/usr/bin/env python
# This example demonstrates the use of VTK data arrays as attribute
# data as well as field data. It creates geometry (vtkPolyData) as
# well as attribute data explicitly.
import vtk
# Create a float array which represents the points.
pcoords = vtk.vtkFloatArray()
# Note that by default, an arr... | CMUSV-VisTrails/WorkflowRecommendation | examples/vtk_examples/DataManipulation/Arrays.py | Python | bsd-3-clause | 2,656 | [
"VTK"
] | bdc30db2d7cb8fb09f6649ddee8d307efe2d512b59f34fde90261473dcdf202a |
from typing import Callable, Iterable, List, Sequence, Tuple, Union, cast
import numpy as np
import tensorflow as tf
from gpflow.base import TensorType
from gpflow.quadrature.deprecated import mvhermgauss
def ndiagquad(
funcs: Union[Callable[..., tf.Tensor], Iterable[Callable[..., tf.Tensor]]],
H: int,
... | GPflow/GPflow | tests/gpflow/quadrature/ndiagquad_old.py | Python | apache-2.0 | 3,267 | [
"Gaussian"
] | dae5bb228802209e2be16affb704d33fc4f61bd020f9744e2209249a115798eb |
"""
Create a profile object from a `numpy.ndarray` of data
======================================================
Use the TAMOC ambient module to create profiles in netCDF format for use by
TAMOC from idealized laboratory data. This file demonstrates working with the
data input directly by the user as a `numpy.ndarra... | socolofs/tamoc | bin/ambient/profile_from_lab.py | Python | mit | 2,237 | [
"NetCDF"
] | f5130c8b5ae0f2ee5482af1827578fe9e2f4c483daaaa88a66e190a45502b418 |
# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
from spack import *
class RMclust(RPackage):
"""Gaussian Mixture Modelling for Model-Based Clustering, Classificatio... | LLNL/spack | var/spack/repos/builtin/packages/r-mclust/package.py | Python | lgpl-2.1 | 1,236 | [
"Gaussian"
] | 831e3eb92103a3df23982dc1ad7b8e43edf55e2e4ae63a1e58faa7fe88e29262 |
# -*- coding: utf-8 -*-
"""
Created on Tue May 31 15:47:34 2016
@author: wxt
"""
from __future__ import division
import copy, collections
import numpy as np
from scipy import sparse
import matplotlib
matplotlib.use('agg')
from tadlib.hitad.aligner import BoundSet, DomainSet, DomainAligner, hierFormat, Container
from ... | XiaoTaoWang/TADLib | tadlib/domaincaller/chromLev.py | Python | gpl-3.0 | 25,346 | [
"Gaussian"
] | 9f4488530b541264e511e86cf136f9736be8466cd7c6188cb6ff0e1543643f31 |
@given(u'I have validated a personal URN')
def step_impl(context):
context.execute_steps(u'''
When I visit "plea/enter_urn/"
And I submit a valid URN
And I fill in "number_of_charges" with "2"
And I fill in correct date of birth
And I press "Continue"
''')
@given(u'I hav... | ministryofjustice/manchester_traffic_offences_pleas | features/steps/steps.py | Python | mit | 1,810 | [
"VisIt"
] | 492c8981bf75b024a46d60043051e887cb890fbb5307a3e186fe50c71b16a578 |
import sys
import math
from optparse import OptionParser, Option, OptionGroup
import scipy
from scipy import random
import numpy
np = numpy
from glue.ligolw import lsctables
from glue.ligolw import utils
from glue.ligolw import ligolw
from glue.ligolw import ilwd
#from glue.segments import segment
from glue.lal import ... | transientlunatic/minke | minke/sources.py | Python | isc | 55,225 | [
"Gaussian"
] | b862dd7c1963f27a1da43a7c3a95d2f6bc2d0b56c118c50ffe0cc2b529d0afcf |
# 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 Bowtie(MakefilePackage):
"""Bowtie is an ultrafast, memory-efficient short read aligner
... | rspavel/spack | var/spack/repos/builtin/packages/bowtie/package.py | Python | lgpl-2.1 | 3,205 | [
"Bowtie"
] | 24a3f9bbf7ddc0e2bf0a82607d40d2e32092fe5fbbcded8c5f4562b66e313944 |
from __future__ import division, absolute_import, print_function
import warnings
import numpy as np
from numpy.testing import (
TestCase, run_module_suite, assert_, assert_raises, assert_equal,
assert_warns, assert_no_warnings, assert_array_equal,
assert_array_almost_equal, suppress_warnings)
f... | ContinuumIO/numpy | numpy/random/tests/test_random.py | Python | bsd-3-clause | 62,019 | [
"Gaussian"
] | 9e34ba764c3dacc78e405c8092e84c4006fcc2e5d9f93c19a6b410b7833606b6 |
###############################################################################
# NARR_to_text.py
# email: ritvik@umd.edu, 24th March, 2015
#
# Convert downloaded data to text
###############################################################################
import constants, util, logging, os, subprocess, pdb, multiproce... | ritviksahajpal/EPIC | NARR/NARR_to_text.py | Python | mit | 6,044 | [
"NetCDF"
] | 81df3b3de1c0cf0a21fc201b58ae21cc89f1e106ddbe8ad9d65348e6f3c60785 |
###############################################################################
# create_EPIC_weather_files.py
# email: ritvik@umd.edu, 24th March, 2015
#
# 1. Download NARR data based on user specified region/site, variables and years
# 2. Convert downloaded data to text and then EPIC compatible weather files
########... | ritviksahajpal/EPIC | NARR/create_EPIC_weather_files.py | Python | mit | 891 | [
"NetCDF"
] | 27a620f8862acab0aa10ae93763647337cc585cf523e526a5b6b6c9981bbbb76 |
import re, os, sys
from optparse import OptionParser
from numpy import *
import subprocess
from communities import *
class ResCluster :
members = []
selection_text = None #selection text for pymol
number = 0 #cluster number
intra_cluster_variance = 0
extra_cluster_variance = 0
indexlist = []
... | chris-lee-mc/MutInf | cg_edgeweights_to_matrix_for_dendro.py | Python | gpl-3.0 | 24,900 | [
"PyMOL"
] | 9d1a268dea9876b252e4dcb04b8f2761abbd248ba74f8068971942a4fcf7aed6 |
#/**********************************************************************
#** This program is part of 'MOOSE', the
#** Messaging Object Oriented Simulation Environment.
#** Copyright (C) 2003-2014 Upinder S. Bhalla. and NCBS
#** It is made available under the terms of the
#** GNU Lesser General Public License... | BhallaLab/moose-examples | paper-2015/Fig2_elecModels/Fig2A.py | Python | gpl-2.0 | 23,553 | [
"Gaussian",
"MOOSE",
"NEURON"
] | e1c5d1cc020392ef76255d1d28bc2974fe768fd02c62b18caa5837129bb72a49 |
from pdbfixer import PDBFixer
from simtk.openmm.app import PDBFile
fixer = PDBFixer(pdbid='3UE4')
fixer.removeChains(chainIds=['B'])
# Without fixer.missingResidues = {}, fixer.addMissingAtoms() throw an exception
# and if I call fixer.findMissingResidues() several terminal residues are added
fixer.missingResidues =... | juliebehr/kinase-benchmark | utils/pdbfix3UE4.py | Python | gpl-2.0 | 546 | [
"OpenMM"
] | 453fea5839bba487e010110b7611e7a8dab82e3f8a78ef8ed855f09c58798cc5 |
'''
PyDelhi App:
- Displays Schedule: static
- Static map:
- Link to open location externally
- Talk/Workshop details
- Feedback
- Social Media:
- Facebook
- Twitter
'''
from datetime import datetime
from kivy.app import App
from kivy.clock import Clock
from kivy.properties import StringProperty
class PyDelhiA... | stalwartrishabh/PyDelhiMobile | pydelhiapp/main.py | Python | agpl-3.0 | 1,599 | [
"VisIt"
] | b379401c6a32d731803e0b5f6ea93b60be9ca0df0eb7741b04887e9c60fb765d |
import vtk
def main():
colors = vtk.vtkNamedColors()
# create a rendering window and renderer
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
# create a renderwindowinteractor
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
styl... | lorensen/VTKExamples | src/Python/Visualization/InteractorStyleTrackballActor.py | Python | apache-2.0 | 962 | [
"VTK"
] | 8d9a44d32216c87b417c754821f89e4ad63af7b8745164cf73317327e53e6d99 |
#
# Licensed to the Apache Software Foundation (ASF) under one or more
# contributor license agreements. See the NOTICE file distributed with
# this work for additional information regarding copyright ownership.
# The ASF licenses this file to You under the Apache License, Version 2.0
# (the "License"); you may not us... | tejasapatil/spark | python/pyspark/ml/regression.py | Python | apache-2.0 | 66,081 | [
"Gaussian"
] | bf59a0ff815b28d5eb0a72a96ffc4203e99652ded53e3deeda2d90e64abae94b |
# Copyright 2016 Autodesk Inc.
#
# 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 writing... | tkzeng/molecular-design-toolkit | moldesign/data.py | Python | apache-2.0 | 8,922 | [
"GAMESS",
"PySCF"
] | 6f47b221cf0c3d74e8623b69ce9af64c91055e8142decc112a938f66be1f1e74 |
#!/usr/bin/python
#
# Copyright 2017 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... | skim1420/spinnaker | google/release/ha_image_janitor.py | Python | apache-2.0 | 8,514 | [
"ORCA"
] | 58229bb5300733761a097fe7e054b5e545c0dc2bf96eb12206178d219753029d |
#!/usr/bin/env python
import pysam
import sys
if __name__ == "__main__":
fmsum = 0
rvsum = 0
ex = sys.argv[0].split("/")[-1]
if len(sys.argv) < 2:
sys.stderr.write("Usage: python %s <bampath> <outfile> "
"[omit outfile to write to stdout]\n" % ex)
sys.exit(1)
... | ARUP-NGS/BMFtools | sample_test/getsums.py | Python | mit | 737 | [
"pysam"
] | 1ba8f7b470ae84271fa367b9e7f50dcbc94c796442e9fc7f8f45ec687eccb603 |
# -*- coding: utf-8 -*-
"""
Created on 26 Sep 2012
@author: Éric Piel
Copyright © 2012-2021 Éric Piel, Philip Winkler, Delmic
This file is part of Odemis.
Odemis is free software: you can redistribute it and/or modify it under the terms
of the GNU General Public License version 2 as published by the Free Software
F... | delmic/odemis | src/odemis/gui/cont/streams.py | Python | gpl-2.0 | 149,861 | [
"Gaussian"
] | 84845e9045fedcc952ce7cf5f3c696507cb5aa0762b021b35ea9f7cfe3789e0d |
# coding: utf-8
# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.
"""
This package implements various diffraction analyses.
"""
__author__ = "Shyue Ping Ong"
__copyright__ = "Copyright 2012, The Materials Project"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
__emai... | fraricci/pymatgen | pymatgen/analysis/diffraction/__init__.py | Python | mit | 366 | [
"pymatgen"
] | cac77d46358f95ab3c9333c2a678061f7636a112a20cf0449e8841d05e93f61c |
"""
PLY-based parser for Myfile grammar.
"""
from __future__ import absolute_import, division, print_function
from mybuild._compat import *
import functools
import itertools
import ply.yacc
from collections import namedtuple, OrderedDict
from mybuild.lang import lex, x_ast as ast
from mybuild.lang.helpers import rule... | abusalimov/mybuild | mybuild/lang/parse.py | Python | mit | 22,275 | [
"VisIt"
] | aca42f6bfa3b5a4f0a73cffdda31e566c10ffc8abbb336cb02965d3399f5db53 |
"""
Manage pools of connections so that we can limit the number of requests per site and reuse
connections.
@since: 1.6
"""
# Copyright (C) 2011, Thomas Leonard
# See the README file for details, or visit http://0install.net.
import sys
if sys.version_info[0] > 2:
from urllib import parse as urlparse # Python 3
els... | rammstein/0install | zeroinstall/injector/scheduler.py | Python | lgpl-2.1 | 5,374 | [
"VisIt"
] | 843fefcae20378440f7a150a3e46ff11905beea19d33d5054bb29d2c36da1dc7 |
# -*- coding: utf-8 -*-
"""
Copyright (C) 2015-2017 Jonathan Taquet
This file is part of Oe2sSLE (Open e2sSample.all Library Editor).
Oe2sSLE 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 t... | JonathanTaquet/Oe2sSLE | GUI/about_dialog.py | Python | gpl-2.0 | 2,870 | [
"VisIt"
] | 75094c52a6d374d8c77e980f439a21ec98af47a4e6957154e97bddce6e36eab0 |
'''
Example of a node that doesn't use Brian at all!
Instead of doing any simulation using Brian, this node only receives and sends back spike trains according to the
formatting used by the BrianConnectUDP.
'''
import numpy
import select
import time
from brian_multiprocess_udp import BrianConnectUDP
my_inputcloc... | ricardodeazambuja/BrianConnectUDP | examples/Brian_Bypass_Node.py | Python | cc0-1.0 | 1,658 | [
"Brian"
] | e2b5c71c9df23b69b1adf5ad7459c5509003fe0bdc8ac9ed9dbef3be90f9533f |
#! /usr/bin/env python
# Copyright 2005 Progeny Linux 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; either version 2 of the License, or
# (at your option) any later version.
#... | blipvert/rpmstrap | tools/rpm_get-arch.py | Python | gpl-2.0 | 5,634 | [
"VisIt"
] | 15696a9724b280d4a0b07bcdee8b7f7fb9d6bb5191f81da05a13ff8964727d58 |
"""Testing for kernels for Gaussian processes."""
# Author: Jan Hendrik Metzen <jhm@informatik.uni-bremen.de>
# License: BSD 3 clause
from collections import Hashable
from sklearn.externals.funcsigs import signature
import numpy as np
from sklearn.gaussian_process.kernels import _approx_fprime
from sklearn.metrics... | toastedcornflakes/scikit-learn | sklearn/gaussian_process/tests/test_kernels.py | Python | bsd-3-clause | 11,602 | [
"Gaussian"
] | 37079c768ba784770c36fc1562cc4afec9e9ff744d2f964fac873393165dfcf9 |
################################################################################
# The Neural Network (NN) based Speech Synthesis System
# https://svn.ecdf.ed.ac.uk/repo/inf/dnn_tts/
#
# Centre for Speech Technology Research
# University of Edinburgh, UK
# ... | bajibabu/merlin | src/work_in_progress/run_dnn_bottleneck.py | Python | apache-2.0 | 52,400 | [
"NEURON"
] | d47b4b21dad0fa56135e90a639265bd5c879d3bede50d28496c36dc932c83b1e |
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