Merge branch 'master' into fix/cell_assembly_detection

NeuralEnsemble · Jul 12, 2023 · 0830333 · 0830333
2 parents 549f89f + 844eb82
commit 0830333
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -1,4 +1,4 @@
-# This workflow will setup GitHub-hosted runners and install the required dependencies for elephant tests.
+# This workflow will set up GitHub-hosted runners and install the required dependencies for elephant tests.
 # On a pull requests and on pushes to master it will run different tests for elephant.
 
 name: tests
@@ -57,8 +57,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # python versions for elephant: [3.7, 3.8, 3.9, "3.10"]
-        python-version: [3.7, 3.8, 3.9, "3.10"]
+        # python versions for elephant: [3.8, 3.9, "3.10", 3.11]
+        python-version: [3.8, 3.9, "3.10", 3.11]
         # OS [ubuntu-latest, macos-latest, windows-latest]
         os: [ubuntu-latest]
       # do not cancel all in-progress jobs if any matrix job fails
@@ -82,7 +82,7 @@ jobs:
       - name: Cache test_env
         uses: actions/cache@v3
         with:
-          path: ~/test_env
+          path: /home/runner/.cache/pip
           # Look to see if there is a cache hit for the corresponding requirements files
           # cache will be reset on changes to any requirements or every month
           key: ${{ runner.os }}-venv-${{ hashFiles('**/requirements.txt') }}-${{ hashFiles('**/requirements-tests.txt') }}
@@ -139,7 +139,7 @@ jobs:
           path: ~/conda_pkgs_dir
           key: ${{ runner.os }}-conda-${{hashFiles('requirements/environment.yml') }}-${{ hashFiles('**/CI.yml') }}-${{ steps.date.outputs.date }}
 
-      - uses: conda-incubator/setup-miniconda@v2.2.0
+      - uses: conda-incubator/setup-miniconda@3b0f2504dd76ef23b6d31f291f4913fb60ab5ff3 # corresponds to v2.2.0
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -181,7 +181,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # python versions for elephant: [3.6, 3.7, 3.8, 3.9]
+        # python versions for elephant: [3.8, 3.9, 3.10, 3.11]
         python-version: [3.8,]
         # OS [ubuntu-latest, macos-latest, windows-latest]
         os: [windows-latest]
@@ -243,7 +243,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # python versions for elephant: [3.6, 3.7, 3.8, 3.9]
+        # python versions for elephant: [3.8, 3.9, 3.10, 3.11]
         python-version: [3.9]
         # OS [ubuntu-latest, macos-latest, windows-latest]
         os: [ubuntu-latest]
@@ -273,6 +273,7 @@ jobs:
 
       - name: Setup environment
         run: |
+          sudo apt-get update
           sudo apt install -y libopenmpi-dev openmpi-bin
 
           python -m pip install --upgrade pip
@@ -331,6 +332,7 @@ jobs:
         run: |
           conda config --add channels conda-forge # bugfix with scipy==1.8.1: libstdcxx-ng 12.1.0 required
           conda update conda
+          conda install -c conda-forge libstdcxx-ng=12 # fix libstdc++.so.6: version for new scipy versions > 1.9.1
           conda env update --file requirements/environment-tests.yml --name base
           activate base
           conda install -c conda-forge openmpi
@@ -387,26 +389,91 @@ jobs:
 
       - name: Install dependencies
         run: |
+          conda config --add channels conda-forge # bugfix with scipy==1.8.1: libstdcxx-ng 12.1.0 required
+          sudo apt-get update
           sudo apt install -y libopenmpi-dev openmpi-bin
+          conda update conda
+          conda install -c conda-forge openmpi pandoc libstdcxx-ng # fix libstdc++.so.6: version for new scipy versions > 1.9.1
+          conda env update --file requirements/environment-docs.yml --name base
+          activate base
           python -m pip install --upgrade pip
           pip install -r requirements/requirements-docs.txt
           pip install -r requirements/requirements-tutorials.txt
-          conda config --add channels conda-forge # bugfix with scipy==1.8.1: libstdcxx-ng 12.1.0 required
-          conda update conda
-          conda env update --file requirements/environment-docs.yml --name base
-          conda install -c conda-forge openmpi
-          conda install -c conda-forge pandoc
           pip install -e .[extras]
           # run notebooks
           sed -i -E "s/nbsphinx_execute *=.*/nbsphinx_execute = 'always'/g" doc/conf.py
 
       - name: List packages
         run: |
+          activate base
           pip list
           conda list
           python --version
 
       - name: make html
         run: |
+          activate base
           cd doc
           make html
+
+  # install dependencies and elephant with pip and run tests with pytest
+  doctests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        # python versions for elephant: [3.7, 3.8, 3.9, "3.10"]
+        python-version: ["3.10"]
+
+        # OS [ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest]
+
+      # do not cancel all in-progress jobs if any matrix job fails
+      fail-fast: false
+
+    steps:
+      # used to reset cache every month
+      - name: Get current year-month
+        id: date
+        run: echo "::set-output name=date::$(date +'%Y-%m')"
+      - uses: actions/checkout@v3
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Cache test_env
+        uses: actions/cache@v3
+        with:
+          path: ~/test_env
+          # Look to see if there is a cache hit for the corresponding requirements files
+          # cache will be reset on changes to any requirements or every month
+          key: ${{ runner.os }}-venv-${{ hashFiles('**/requirements.txt') }}-${{ hashFiles('**/requirements-tests.txt') }}
+            -${{ hashFiles('**/requirements-extras.txt') }}-${{ hashFiles('**/CI.yml') }}-${{ hashFiles('setup.py') }}
+            -${{ steps.date.outputs.date }}
+
+      - name: Install dependencies
+        run: |
+          # create an environment and install everything
+          python -m venv ~/test_env
+          source ~/test_env/bin/activate
+          sudo apt install -y libopenmpi-dev openmpi-bin
+
+          python -m pip install --upgrade pip
+          pip install mpi4py
+          pip install -r requirements/requirements-tests.txt
+          pip install -r requirements/requirements.txt
+          pip install -r requirements/requirements-extras.txt
+          pip install pytest-cov coveralls
+          pip install -e .
+
+      - name: List packages
+        run: |
+          source ~/test_env/bin/activate
+          pip list
+          python --version
+
+      - name: Run doctests
+        run: |
+          source ~/test_env/bin/activate
+          pytest elephant --doctest-modules --ignore=elephant/test/
diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
@@ -33,8 +33,8 @@ 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@v3

diff --git a/.github/workflows/ebrains.yml b/.github/workflows/ebrains.yml
@@ -10,15 +10,15 @@ jobs:
     if: ${{ github.repository_owner == 'NeuralEnsemble' }}
     steps:
       - name: syncmaster
-        uses: wei/git-sync@v3
+        uses: wei/git-sync@55c6b63b4f21607da0e9877ca9b4d11a29fc6d83 # corresponds to v3
         with:
           source_repo: "NeuralEnsemble/elephant"
           source_branch: "master"
           destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/neuralensemble/elephant.git"
           destination_branch: "master"
 
       - name: synctags
-        uses: wei/git-sync@v3
+        uses: wei/git-sync@55c6b63b4f21607da0e9877ca9b4d11a29fc6d83 # corresponds to v3
         with:
           source_repo: "NeuralEnsemble/elephant"
           source_branch: "refs/tags/*"

diff --git a/.gitignore b/.gitignore
@@ -83,6 +83,8 @@ 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
@@ -10,26 +10,6 @@
             "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": "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",
-            "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"
-        },
-        {
-            "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": "Bouss, Peter"
-        },
-        {
-            "orcid": "0000-0002-3818-5587",
-            "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"
-        },
         {
             "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",
@@ -40,15 +20,6 @@
             "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"
         },
-        {
-            "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": "Kloß, Oliver"
-        },
-        {
-            "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": "0000-0001-7292-1982",
             "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",
@@ -60,23 +31,13 @@
             "name": "Kurth, Anno Christopher"
         },
         {
-            "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 0.11.2",
+    "title": "Elephant 0.12.0",
 
     "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
@@ -1,6 +1,5 @@
 # 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/)
@@ -9,6 +8,7 @@
 [![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)
 
 *Elephant* package analyses all sorts of neurophysiological data:
 spike trains, LFP, analog signals. The input-output data format is either
@@ -35,7 +35,7 @@ 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