Merge branch 'master' into fix_exlude_examples

BlueBrain · Jun 19, 2024 · 4a2c167 · 4a2c167
2 parents ed2863f + aff67f8
commit 4a2c167
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diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -12,9 +12,9 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ["3.8", "3.9", "3.10", "3.11"]
+        python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
         include:
-          - os: macos-latest
+          - os: macos-12
             python-version: "3.10"
 
     steps:

diff --git a/.install_neuron.sh b/.install_neuron.sh
diff --git a/.jenkins.sh b/.jenkins.sh
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -14,3 +14,8 @@ python:
     - method: pip
       path: .
     - requirements: requirements_docs.txt
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
diff --git a/.zenodo.json b/.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"
+    }
+  ]
+}
diff --git a/README.rst b/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
diff --git a/bluepyopt/deapext/tools/selIBEA.py b/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: