Merge branch 'master' into fix/bibtex-contrib-version-cap

INM-6 · Feb 6, 2023 · 65fedf2 · 65fedf2
2 parents ace0fec + 0896873
commit 65fedf2
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Showing 27 changed files with 385 additions and 157 deletions.
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: ${{ matrix.os }}
     strategy:
       matrix:
-        # python versions for elephant: [3.7, 3.8, 3.9, "3.10"]
-        python-version: [3.7, 3.8, 3.9, "3.10"]
+        # python versions for elephant: [3.8, 3.9, "3.10", 3.11]
+        python-version: [3.8, 3.9, "3.10", 3.11]
         # OS [ubuntu-latest, macos-latest, windows-latest]
         os: [ubuntu-latest]
       # do not cancel all in-progress jobs if any matrix job fails
@@ -68,7 +68,7 @@ jobs:
       # used to reset cache every month
       - name: Get current year-month
         id: date
-        run: echo "::set-output name=date::$(date +'%Y-%m')"
+        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
 
       - uses: actions/checkout@v3
 
@@ -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') }}-${{ hashFiles('**/requirements-tests.txt') }}
@@ -129,7 +129,7 @@ jobs:
     steps:
       - name: Get current year-month
         id: date
-        run: echo "::set-output name=date::$(date +'%Y-%m')"
+        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
 
       - uses: actions/checkout@v3
 
@@ -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
+      - uses: conda-incubator/setup-miniconda@v2.2.0
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
@@ -181,7 +181,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # python versions for elephant: [3.6, 3.7, 3.8, 3.9]
+        # python versions for elephant: [3.8, 3.9, 3.10, 3.11]
         python-version: [3.8,]
         # OS [ubuntu-latest, macos-latest, windows-latest]
         os: [windows-latest]
@@ -198,7 +198,7 @@ jobs:
     steps:
       - name: Get current year-month
         id: date
-        run: echo "::set-output name=date::$(date +'%Y-%m')"
+        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
 
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
@@ -243,7 +243,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        # python versions for elephant: [3.6, 3.7, 3.8, 3.9]
+        # python versions for elephant: [3.8, 3.9, 3.10, 3.11]
         python-version: [3.9]
         # OS [ubuntu-latest, macos-latest, windows-latest]
         os: [ubuntu-latest]
@@ -254,7 +254,7 @@ jobs:
     steps:
       - name: Get current year-month
         id: date
-        run: echo "::set-output name=date::$(date +'%Y-%m')"
+        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
       - uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
@@ -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
@@ -368,7 +370,7 @@ jobs:
 
       - name: Get current year-month
         id: date
-        run: echo "::set-output name=date::$(date +'%Y-%m')"
+        run: echo "date=$(date +'%Y-%m')" >> $GITHUB_OUTPUT
 
       - uses: actions/checkout@v3
 
@@ -387,6 +389,7 @@ jobs:
 
       - name: Install dependencies
         run: |
+          sudo apt-get update
           sudo apt install -y libopenmpi-dev openmpi-bin
           python -m pip install --upgrade pip
           pip install -r requirements/requirements-docs.txt

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/.zenodo.json b/.zenodo.json
@@ -41,7 +41,6 @@
             "name": "Kramer, Maximilian"
         },
         {
-            "orcid": "",
             "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"
         },

diff --git a/doc/conf.py b/doc/conf.py
@@ -33,7 +33,6 @@
     'sphinx.ext.doctest',
     'sphinx.ext.intersphinx',
     'sphinx.ext.todo',
-    'sphinx.ext.imgmath',
     'sphinx.ext.viewcode',
     'sphinx.ext.mathjax',
     'sphinxcontrib.bibtex',
@@ -350,8 +349,8 @@
     'numpy': ('https://numpy.org/doc/stable', None)
 }
 
-# Use more reliable mathjax source
-mathjax_path = 'https://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
+# The name of math_renderer extension for HTML output.
+html_math_renderer = 'mathjax'
 
 
 def process_docstring_remove_copyright(app, what, name, obj, options, lines):

diff --git a/doc/install.rst b/doc/install.rst
@@ -14,7 +14,7 @@ Below is the explanation of how to proceed with these two steps.
 Prerequisites
 *************
 
-Elephant requires `Python <http://python.org/>`_ 3.7, 3.8, 3.9 or 3.10.
+Elephant requires `Python <http://python.org/>`_ 3.8, 3.9, 3.10 or 3.11.
 
 .. tabs::
 
@@ -25,7 +25,7 @@ Elephant requires `Python <http://python.org/>`_ 3.7, 3.8, 3.9 or 3.10.
 
            .. code-block:: sh
 
-              conda create --name elephant python=3.7 numpy scipy tqdm
+              conda create --name elephant python=3.8 numpy scipy tqdm
 
         2. Activate your environment: