Merge branch 'master' into numpy-scaler

.zenodo.json

@@ -0,0 +1,48 @@
+{
+  "title" : "BluePyOpt",
+  "license": "LGPL-3.0",
+  "upload_type": "software",
+  "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.",
+  "creators": [
+    {
+      "affiliation": "Blue Brain Project, EPFL",
+      "name": "Van Geit, Werner",
+      "orcid": "0000-0002-2915-720X"
+    },
+    {
+      "affiliation": "Blue Brain Project, EPFL",
+      "name": "Gevaert, Michael",
+      "orcid": "0000-0002-7547-3297"
+    },
+    {
+      "affiliation": "Blue Brain Project, EPFL",
+      "name": "Damart, Tanguy",
+      "orcid": "0000-0003-2175-7304"
+    },
+    {
+      "affiliation": "Blue Brain Project, EPFL",
+      "name": "Rössert, Christian",
+      "orcid": "0000-0002-4839-2424"
+    },
+    {
+      "affiliation": "Blue Brain Project, EPFL",
+      "name": "Courcol, Jean-Denis",
+      "orcid": "0000-0002-9351-1461"
+    },
+    {
+      "affiliation": "Blue Brain Project, EPFL",
+      "name": "Chindemi, Guiseppe",
+      "orcid": "0000-0001-6872-2366"
+    },
+    {
+      "affiliation": "Blue Brain Project, EPFL",
+      "name": "Jaquier, Aurélien",
+      "orcid": "0000-0001-6202-6175"
+    },
+    {
+      "affiliation": "Blue Brain Project, EPFL",
+      "name": "Muller, Eilif",
+      "orcid": "0000-0003-4309-8266"
+    }
+  ]
+}

README.rst

@@ -3,59 +3,22 @@
 BluePyOpt
 =========
 
-.. raw:: html
-
-	<table>
-	<tr>
-	  <td>Latest Release</td>
-	  <td>
-	    <a href="https://pypi.org/project/bluepyopt/">
-	    <img src="https://img.shields.io/pypi/v/bluepyopt.svg" alt="latest release" />
-	    </a>
-	  </td>
-	</tr>
-	<tr>
-	  <td>Documentation</td>
-	  <td>
-	    <a href="https://bluepyopt.readthedocs.io/">
-	    <img src="https://readthedocs.org/projects/bluepyopt/badge/?version=latest" alt="latest documentation" />
-	    </a>
-	  </td>
-	</tr>
-	<tr>
-	  <td>License</td>
-	  <td>
-	    <a href="https://github.com/BlueBrain/bluepyopt/blob/master/LICENSE.txt">
-	    <img src="https://img.shields.io/pypi/l/bluepyopt.svg" alt="license" />
-	    </a>
-	</td>
-	</tr>
-	<tr>
-	  <td>Build Status</td>
-	  <td>
-	    <a href="https://github.com/BlueBrain/BluePyOpt/actions">
-	    <img src="https://github.com/BlueBrain/BluePyOpt/workflows/Build/badge.svg?branch=master" alt="Actions build status" />
-	    </a>
-	  </td>
-	</tr>
-	<tr>
-	  <td>Coverage</td>
-	  <td>
-	    <a href="https://codecov.io/gh/BlueBrain/bluepyopt">
-	    <img src="https://codecov.io/github/BlueBrain/BluePyOpt/coverage.svg?branch=master" alt="coverage" />
-	    </a>
-	  </td>
-	</tr>
-	<tr>
-		<td>Gitter</td>
-		<td>
-			<a href="https://gitter.im/bluebrain/bluepyopt">
-			<img src="https://badges.gitter.im/Join%20Chat.svg"
-		</a>
-		</td>
-	</tr>
-	</table>
 
++----------------+------------+
+| Latest Release | |pypi|     |
++----------------+------------+
+| Documentation  | |docs|     |
++----------------+------------+
+| License        | |license|  |
++----------------+------------+
+| Build Status 	 | |build|    |
++----------------+------------+
+| Coverage       | |coverage| |
++----------------+------------+
+| Gitter         | |gitter|   |
++----------------+------------+
+| Zenodo         | |zenodo|   |
++----------------+------------+
 
 
 Introduction
@@ -229,6 +192,33 @@ Copyright (c) 2016-2022 Blue Brain Project/EPFL
     The index.rst location is used for the docs README; index.rst also defined an end-marker, 
     to skip content after the marker 'substitutions'.
 
+.. |pypi| image:: https://img.shields.io/pypi/v/bluepyopt.svg
+               :target: https://pypi.org/project/bluepyopt/
+               :alt: latest release
+
+.. |docs| image:: https://readthedocs.org/projects/bluepyopt/badge/?version=latest
+               :target: https://bluepyopt.readthedocs.io/
+               :alt: latest documentation
+
+.. |license| image:: https://img.shields.io/pypi/l/bluepyopt.svg
+                  :target: https://github.com/BlueBrain/bluepyopt/blob/master/LICENSE.txt
+                  :alt: license
+
+.. |build| image:: https://github.com/BlueBrain/BluePyOpt/workflows/Build/badge.svg?branch=master
+                :target: https://github.com/BlueBrain/BluePyOpt/actions
+                :alt: actions build status
+
+.. |coverage| image:: https://codecov.io/github/BlueBrain/BluePyOpt/coverage.svg?branch=master
+                   :target: https://codecov.io/gh/BlueBrain/bluepyopt
+                   :alt: coverage
+
+.. |gitter| image:: https://badges.gitter.im/Join%20Chat.svg
+                 :target: https://gitter.im/BlueBrain/blueptopt
+                 :alt: Join the chat at https://gitter.im/BlueBrain/BluePyOpt
+
+.. |zenodo| image:: https://zenodo.org/badge/DOI/10.5281/zenodo.8135890.svg
+                :target: https://doi.org/10.5281/zenodo.8135890
+
 .. substitutions
 .. |banner| image:: docs/source/logo/BluePyOptBanner.png
 .. |landscape_example| image:: examples/simplecell/figures/landscape_example.png

bluepyopt/deapext/tools/selIBEA.py

@@ -1,9 +1,5 @@
 """IBEA selector"""
 
-from __future__ import division
-
-from past.builtins import xrange  # pylint: disable=W0622
-
 """
 Copyright (c) 2016-2022, EPFL/Blue Brain Project
 
@@ -77,7 +73,7 @@ def _calc_fitness_components(population, kappa):
     box_ranges[box_ranges == 0] = 1.0
 
     components_matrix = numpy.zeros((pop_len, pop_len))
-    for i in xrange(0, pop_len):
+    for i in range(0, pop_len):
         diff = population_matrix - population_matrix[i, :]
         components_matrix[i, :] = numpy.max(
             numpy.divide(diff, box_ranges),
@@ -115,9 +111,9 @@ def _mating_selection(population, mu, tournament_n):
     """Returns the n_of_parents individuals with the best fitness"""
 
     parents = []
-    for _ in xrange(mu):
+    for _ in range(mu):
         winner = _choice(population)
-        for _ in xrange(tournament_n - 1):
+        for _ in range(tournament_n - 1):
             individual = _choice(population)
             # Save winner is element with smallest fitness
             if individual.ibea_fitness < winner.ibea_fitness:

bluepyopt/ephys/efeatures.py

@@ -429,6 +429,11 @@ def calculate_feature(
         peak_times = self._get_peak_times(
             responses, raise_warnings=raise_warnings
         )
+        if peak_times is None:
+            if return_waveforms:
+                return None, None
+            else:
+                return None
 
         if len(peak_times) > 1 and self.skip_first_spike:
             peak_times = peak_times[1:]
@@ -439,7 +444,10 @@ def calculate_feature(
         if responses[self.recording_names[""]] is not None:
             response = responses[self.recording_names[""]]
         else:
-            return None
+            if return_waveforms:
+                return None, None
+            else:
+                return None
 
         if np.std(np.diff(response["time"])) > 0.001 * np.mean(
                 np.diff(response["time"])

bluepyopt/ephys/serializer.py

@@ -1,8 +1,4 @@
 '''Mixin class to make dictionaries'''
-from __future__ import unicode_literals
-from __future__ import print_function
-from __future__ import division
-from __future__ import absolute_import
 
 # Disabling lines below, generate error when loading ephys.examples
 # from future import standard_library

bluepyopt/ipyp/bpopt_tasksdb.py

@@ -1,7 +1,5 @@
 """Get stats out of ipyparallel's tasks.db"""
 
-from __future__ import print_function
-
 """
 Copyright (c) 2016-2020, EPFL/Blue Brain Project
 

examples/graupnerbrunelstdp/run_fit.py

@@ -2,8 +2,6 @@
 
 # pylint: disable=R0914
 
-from __future__ import print_function
-
 import pickle
 import bluepyopt as bpop
 import matplotlib.pyplot as plt