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Merge branch 'master' into numpy-scaler
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‎.install_neuron.sh‎

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‎.jenkins.sh‎

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‎.zenodo.json‎

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{
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"title" : "BluePyOpt",
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"license": "LGPL-3.0",
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"upload_type": "software",
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"description": "The Blue Brain Python Optimisation Library (BluePyOpt) is an extensible framework for data-driven model parameter optimisation that wraps and standardises several existing open-source tools. It simplifies the task of creating and sharing these optimisations, and the associated techniques and knowledge. This is achieved by abstracting the optimisation and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. Further, BluePyOpt provides methods for setting up both small- and large-scale optimisations on a variety of platforms, ranging from laptops to Linux clusters and cloud-based compute infrastructures.",
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"creators": [
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{
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"affiliation": "Blue Brain Project, EPFL",
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"name": "Van Geit, Werner",
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"orcid": "0000-0002-2915-720X"
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},
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{
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"affiliation": "Blue Brain Project, EPFL",
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"name": "Gevaert, Michael",
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"orcid": "0000-0002-7547-3297"
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},
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{
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"affiliation": "Blue Brain Project, EPFL",
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"name": "Damart, Tanguy",
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"orcid": "0000-0003-2175-7304"
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},
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{
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"affiliation": "Blue Brain Project, EPFL",
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"name": "Rössert, Christian",
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"orcid": "0000-0002-4839-2424"
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},
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{
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"affiliation": "Blue Brain Project, EPFL",
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"name": "Courcol, Jean-Denis",
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"orcid": "0000-0002-9351-1461"
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},
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{
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"affiliation": "Blue Brain Project, EPFL",
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"name": "Chindemi, Guiseppe",
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"orcid": "0000-0001-6872-2366"
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},
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{
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"affiliation": "Blue Brain Project, EPFL",
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"name": "Jaquier, Aurélien",
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"orcid": "0000-0001-6202-6175"
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},
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{
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"affiliation": "Blue Brain Project, EPFL",
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"name": "Muller, Eilif",
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"orcid": "0000-0003-4309-8266"
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}
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]
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}

‎README.rst‎

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BluePyOpt
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=========
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.. raw:: html
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<table>
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<tr>
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<td>Latest Release</td>
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<td>
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<a href="https://pypi.org/project/bluepyopt/">
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<img src="https://img.shields.io/pypi/v/bluepyopt.svg" alt="latest release" />
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</a>
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</td>
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</tr>
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<tr>
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<td>Documentation</td>
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<td>
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<a href="https://bluepyopt.readthedocs.io/">
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<img src="https://readthedocs.org/projects/bluepyopt/badge/?version=latest" alt="latest documentation" />
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</a>
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</td>
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</tr>
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<tr>
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<td>License</td>
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<td>
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<a href="https://github.com/BlueBrain/bluepyopt/blob/master/LICENSE.txt">
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<img src="https://img.shields.io/pypi/l/bluepyopt.svg" alt="license" />
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</a>
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</td>
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</tr>
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<tr>
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<td>Build Status</td>
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<td>
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<a href="https://github.com/BlueBrain/BluePyOpt/actions">
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<img src="https://github.com/BlueBrain/BluePyOpt/workflows/Build/badge.svg?branch=master" alt="Actions build status" />
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</a>
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</td>
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</tr>
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<tr>
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<td>Coverage</td>
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<td>
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<a href="https://codecov.io/gh/BlueBrain/bluepyopt">
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<img src="https://codecov.io/github/BlueBrain/BluePyOpt/coverage.svg?branch=master" alt="coverage" />
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</a>
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</td>
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</tr>
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<tr>
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<td>Gitter</td>
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<td>
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<a href="https://gitter.im/bluebrain/bluepyopt">
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<img src="https://badges.gitter.im/Join%20Chat.svg"
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</a>
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</td>
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</tr>
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</table>
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+----------------+------------+
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| Latest Release | |pypi| |
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+----------------+------------+
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| Documentation | |docs| |
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+----------------+------------+
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| License | |license| |
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+----------------+------------+
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| Build Status | |build| |
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+----------------+------------+
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| Coverage | |coverage| |
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+----------------+------------+
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| Gitter | |gitter| |
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+----------------+------------+
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| Zenodo | |zenodo| |
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+----------------+------------+
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Introduction
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The index.rst location is used for the docs README; index.rst also defined an end-marker,
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to skip content after the marker 'substitutions'.
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.. |pypi| image:: https://img.shields.io/pypi/v/bluepyopt.svg
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:target: https://pypi.org/project/bluepyopt/
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:alt: latest release
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.. |docs| image:: https://readthedocs.org/projects/bluepyopt/badge/?version=latest
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:target: https://bluepyopt.readthedocs.io/
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:alt: latest documentation
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.. |license| image:: https://img.shields.io/pypi/l/bluepyopt.svg
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:target: https://github.com/BlueBrain/bluepyopt/blob/master/LICENSE.txt
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:alt: license
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.. |build| image:: https://github.com/BlueBrain/BluePyOpt/workflows/Build/badge.svg?branch=master
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:target: https://github.com/BlueBrain/BluePyOpt/actions
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:alt: actions build status
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.. |coverage| image:: https://codecov.io/github/BlueBrain/BluePyOpt/coverage.svg?branch=master
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:target: https://codecov.io/gh/BlueBrain/bluepyopt
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:alt: coverage
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.. |gitter| image:: https://badges.gitter.im/Join%20Chat.svg
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:target: https://gitter.im/BlueBrain/blueptopt
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:alt: Join the chat at https://gitter.im/BlueBrain/BluePyOpt
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.. |zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.8135890.svg
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:target: https://doi.org/10.5281/zenodo.8135890
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.. substitutions
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.. |banner| image:: docs/source/logo/BluePyOptBanner.png
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.. |landscape_example| image:: examples/simplecell/figures/landscape_example.png

‎bluepyopt/deapext/tools/selIBEA.py‎

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"""IBEA selector"""
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from past.builtins import xrange # pylint: disable=W0622
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"""
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Copyright (c) 2016-2022, EPFL/Blue Brain Project
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box_ranges[box_ranges == 0] = 1.0
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components_matrix = numpy.zeros((pop_len, pop_len))
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for i in xrange(0, pop_len):
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for i in range(0, pop_len):
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diff = population_matrix - population_matrix[i, :]
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components_matrix[i, :] = numpy.max(
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numpy.divide(diff, box_ranges),
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"""Returns the n_of_parents individuals with the best fitness"""
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parents = []
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for _ in xrange(mu):
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for _ in range(mu):
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winner = _choice(population)
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for _ in xrange(tournament_n - 1):
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for _ in range(tournament_n - 1):
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individual = _choice(population)
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# Save winner is element with smallest fitness
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if individual.ibea_fitness < winner.ibea_fitness:

‎bluepyopt/ephys/efeatures.py‎

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peak_times = self._get_peak_times(
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if peak_times is None:
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if return_waveforms:
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return None, None
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else:
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return None
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peak_times = peak_times[1:]
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if responses[self.recording_names[""]] is not None:
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response = responses[self.recording_names[""]]
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return None
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if return_waveforms:
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return None, None
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else:
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return None
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if np.std(np.diff(response["time"])) > 0.001 * np.mean(
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np.diff(response["time"])

‎bluepyopt/ephys/serializer.py‎

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'''Mixin class to make dictionaries'''
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from __future__ import unicode_literals
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from __future__ import print_function
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from __future__ import division
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# from future import standard_library

‎bluepyopt/ipyp/bpopt_tasksdb.py‎

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"""Get stats out of ipyparallel's tasks.db"""
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"""
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Copyright (c) 2016-2020, EPFL/Blue Brain Project
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‎examples/graupnerbrunelstdp/run_fit.py‎

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# pylint: disable=R0914
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import pickle
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import bluepyopt as bpop
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import matplotlib.pyplot as plt

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