Merge branch 'master' into master

NeuralEnsemble · Sep 25, 2023 · a1ff672 · a1ff672
2 parents 4f71560 + c3eb21f
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
@@ -1,13 +1,12 @@
 name: Build Wheels
 
-# Trigger the workflow on push or pull request of the master
+# Trigger the workflow on push to master. (this is equal to: PR is merged)
 on:
   push:
     branches:
       - master
-  pull_request:
-    branches:
-      - master
+  pull_request_review:
+    types: [ submitted ]
 
 # Building wheels on Ubuntu and Windows systems
 jobs:
@@ -19,10 +18,10 @@ jobs:
         os: [ubuntu-20.04, windows-2019]
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       # Used to host cibuildwheel
-      - uses: actions/setup-python@v2
+      - uses: actions/setup-python@v4
 
       - name: Install cibuildwheel
         run: python -m pip install cibuildwheel==2.3.1
@@ -34,10 +33,10 @@ jobs:
       - name: Build wheels
         run: python -m cibuildwheel --output-dir wheelhouse
         env:
-          CIBW_SKIP: "cp27-* cp33-* cp34-* cp35-* cp36-* pp*"
-          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.7"
+          CIBW_SKIP: "cp27-* cp33-* cp34-* cp35-* cp36-* cp37-* pp*"
+          CIBW_PROJECT_REQUIRES_PYTHON: ">=3.8"
           CIBW_ARCHS: "auto64"
 
-      - uses: actions/upload-artifact@v2
+      - uses: actions/upload-artifact@v3
         with:
           path: ./wheelhouse/*.whl
diff --git a/.github/workflows/ebrains.yml b/.github/workflows/ebrains.yml
@@ -0,0 +1,26 @@
+name: Mirror to EBRAINS
+
+on:
+  push:
+    branches: [ master ]
+
+jobs:
+  sync_to_ebrains:
+    runs-on: ubuntu-latest
+    if: ${{ github.repository_owner == 'NeuralEnsemble' }}
+    steps:
+      - name: syncmaster
+        uses: wei/git-sync@55c6b63b4f21607da0e9877ca9b4d11a29fc6d83 # corresponds to v3
+        with:
+          source_repo: "NeuralEnsemble/elephant"
+          source_branch: "master"
+          destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/neuralensemble/elephant.git"
+          destination_branch: "master"
+
+      - name: synctags
+        uses: wei/git-sync@55c6b63b4f21607da0e9877ca9b4d11a29fc6d83 # corresponds to v3
+        with:
+          source_repo: "NeuralEnsemble/elephant"
+          source_branch: "refs/tags/*"
+          destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/neuralensemble/elephant.git"
+          destination_branch: "refs/tags/*"
diff --git a/.gitignore b/.gitignore
@@ -20,6 +20,7 @@ venv/
 env/
 .pytest_cache/
 **/*/__pycache__
+*.vscode
 
 # Compiled source #
 ###################
@@ -83,6 +84,8 @@ ignored/
 
 # data
 *.nix
+*.csv
+*.mat
 
 # neo logs
 **/logs
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
@@ -0,0 +1,11 @@
+# This workflow will be executed on gitlab and trigger the spack build process
+# on commit to master branch on github NeuralEnsemble master branch.
+stages:          # List of stages for jobs, and their order of execution
+  - build
+
+build-job:       # This job runs in the build stage, which runs first.
+  stage: build
+  script:
+    - curl -X POST --fail -F "token=$EBRAINS_SPACK_BUILD_TRIGGER" -F "ref=feature/dev_version" https://gitlab.ebrains.eu/api/v4/projects/322/trigger/pipeline
+  tags:
+    - shell-runner
diff --git a/.zenodo.json b/.zenodo.json
@@ -11,68 +11,53 @@
             "name": "Köhler, Cristiano"
         },
         {
-            "orcid": "0000-0002-2403-928X",
-            "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
-            "name": "Morales-Gregorio, Aitor"
-        },
-        {
-            "orcid": "0000-0003-3776-4226",
+            "orcid": "0000-0003-0789-6279",
             "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
-            "name": "Kleinjohann, Alexander"
+            "name": "Jurkus, Regimantas"
         },
         {
-            "orcid": "0000-0003-2498-0536",
+            "orcid": "0000-0001-7292-1982",
             "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
-            "name": "Bouss, Peter"
+            "name": "Kern, Moritz"
         },
         {
-            "orcid": "0000-0002-3818-5587",
+            "orcid": "0000-0002-9557-1003",
             "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
-            "name": "Stella, Alessandra"
+            "name": "Kurth, Anno Christopher"
         },
         {
-            "orcid": "0000-0003-0789-6279",
+            "orcid": "0000-0003-3776-4226",
             "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
-            "name": "Jurkus, Regimantas"
+            "name": "Kleinjohann, Alexander"
         },
         {
-            "orcid": "0000-0002-9302-5893",
+            "orcid": "0000-0003-2498-0536",
             "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
-            "name": "Kramer, Maximilian"
+            "name": "Bouss, Peter"
         },
         {
-            "orcid": "0000-0002-5555-3206",
-            "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
-            "name": "Dąbrowska, Paulina"
+            "orcid": "0000-0002-4793-7541",
+            "affiliation": "Institut des Neurosciences Paris-Saclay (NeuroPSI), Département de Neurosciences Intégratives et Computationnelles (ICN), Université Paris-Saclay, France",
+            "name": "Davison, Andrew"
         },
         {
-            "orcid": "0000-0001-7292-1982",
+            "orcid": "0000-0002-2403-928X",
             "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
-            "name": "Kern, Moritz"
+            "name": "Morales-Gregorio, Aitor"
         },
         {
-            "orcid": "0000-0002-9557-1003",
+            "orcid": "0000-0002-9302-5893",
             "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
-            "name": "Kurth, Anno Christopher"
+            "name": "Kramer, Maximilian"
         },
         {
-            "orcid": "0000-0001-7373-5962",
+            "orcid": "0000-0001-9170-4422",
             "affiliation": "Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany",
-            "name": "Gutzen, Robin"
-        },
-        {
-            "orcid": "0000-0003-2401-7862",
-            "affiliation": "Cognitronics and Sensor Systems, CITEC, Bielefeld University, Bielefeld, Germany",
-            "name": "Porrmann, Florian"
-        },
-        {
-            "orcid": "0000-0002-3168-7365",
-            "affiliation": "Cognitronics and Sensor Systems, CITEC, Bielefeld University, Bielefeld, Germany",
-            "name": "Pilz, Sarah"
+            "name": "Ito, Junji"
         }
     ],
 
-    "title": "Elephant 0.11.1",
+    "title": "Elephant 0.13.0",
 
     "keywords": [
     "neuroscience",

diff --git a/LICENSE.txt b/LICENSE.txt
@@ -1,4 +1,4 @@
-Copyright (c) 2014-2022, Elephant authors and contributors
+Copyright (c) 2014-2023, Elephant authors and contributors
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:
@@ -7,4 +7,4 @@ Redistribution and use in source and binary forms, with or without modification,
 * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
 * Neither the names of the copyright holders nor the names of the contributors may be used to endorse or promote products derived from this software without specific prior written permission.
 
-THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
diff --git a/README.md b/README.md
@@ -1,13 +1,17 @@
 # Elephant - Electrophysiology Analysis Toolkit
 
-[![Build Status](https://travis-ci.org/NeuralEnsemble/elephant.svg?branch=master)](https://travis-ci.org/NeuralEnsemble/elephant)
 [![Coverage Status](https://coveralls.io/repos/github/NeuralEnsemble/elephant/badge.svg?branch=master)](https://coveralls.io/github/NeuralEnsemble/elephant?branch=master)
 [![Documentation Status](https://readthedocs.org/projects/elephant/badge/?version=latest)](https://elephant.readthedocs.io/en/latest/?badge=latest)
 [![![PyPi]](https://img.shields.io/pypi/v/elephant)](https://pypi.org/project/elephant/)
 [![Statistics](https://img.shields.io/pypi/dm/elephant)](https://seladb.github.io/StarTrack-js/#/preload?r=neuralensemble,elephant)
 [![Gitter](https://badges.gitter.im/python-elephant/community.svg)](https://gitter.im/python-elephant/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge)
 [![DOI Latest Release](https://zenodo.org/badge/10311278.svg)](https://zenodo.org/badge/latestdoi/10311278)
 [![tests](https://github.com/NeuralEnsemble/elephant/actions/workflows/CI.yml/badge.svg)](https://github.com/NeuralEnsemble/elephant/actions/workflows/CI.yml)
+[![CII Best Practices](https://bestpractices.coreinfrastructure.org/projects/6191/badge)](https://bestpractices.coreinfrastructure.org/projects/6191)
+[![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu)
+[![Twitter](https://img.shields.io/twitter/follow/PyElephant?style=social)](https://twitter.com/pyelephant)
+[![Fosstodon](https://img.shields.io/badge/@elephant-6364FF?logo=mastodon&logoColor=fff&style=flat)](https://fosstodon.org/@elephant)
+
 
 *Elephant* package analyses all sorts of neurophysiological data:
 spike trains, LFP, analog signals. The input-output data format is either
@@ -34,7 +38,7 @@ Modified BSD License, see [LICENSE.txt](LICENSE.txt) for details.
 
 #### Copyright
 
-:copyright: 2014-2022 by the [Elephant team](doc/authors.rst).
+:copyright: 2014-2023 by the [Elephant team](doc/authors.rst).
 
 
 #### Acknowledgments
@@ -44,4 +48,4 @@ See [acknowledgments](doc/acknowledgments.rst).
 
 #### Citation
 
-See [citations](doc/citation.rst).
+See [citations](doc/citation.rst).