Merge remote-tracking branch 'upstream/master' into integrate_odes_hi…

…gh_order
nest · Nov 7, 2024 · 29c856f · 29c856f
2 parents 6c9e5dd + 3d0d087
commit 29c856f
Show file tree

Hide file tree

Showing 5 changed files with 101 additions and 103 deletions.
diff --git a/.github/workflows/continuous_benchmarking_master_branch.yml b/.github/workflows/continuous_benchmarking_master_branch.yml
@@ -0,0 +1,82 @@
+on:
+  push:
+    branches: master
+
+jobs:
+  benchmark_base_branch:
+    name: Continuous Benchmarking Fork PRs with Bencher
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          ref: ${{ github.event.pull_request.head.sha }}
+          persist-credentials: false
+
+      - uses: bencherdev/bencher@main
+
+      # Setup Python version
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.9
+
+      # Install dependencies
+      - name: Install apt dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install libltdl7-dev libgsl0-dev libncurses5-dev libreadline6-dev pkg-config
+          sudo apt-get install python3-all-dev python3-matplotlib python3-numpy python3-scipy ipython3
+
+      # Install Python dependencies
+      - name: Python dependencies
+        run: |
+          python -m pip install --upgrade pip pytest jupyterlab matplotlib pycodestyle scipy pandas pytest-benchmark
+          python -m pip install -r requirements.txt
+
+      # Install NEST simulator
+      - name: NEST simulator
+        run: |
+          python -m pip install cython
+          echo "GITHUB_WORKSPACE = $GITHUB_WORKSPACE"
+          NEST_SIMULATOR=$(pwd)/nest-simulator
+          NEST_INSTALL=$(pwd)/nest_install
+          echo "NEST_SIMULATOR = $NEST_SIMULATOR"
+          echo "NEST_INSTALL = $NEST_INSTALL"
+
+          git clone --depth=1 https://github.com/nest/nest-simulator
+          mkdir nest_install
+          echo "NEST_INSTALL=$NEST_INSTALL" >> $GITHUB_ENV
+          cd nest_install
+          cmake -DCMAKE_INSTALL_PREFIX=$NEST_INSTALL $NEST_SIMULATOR
+          make && make install
+          cd ..
+
+      # Install NESTML (repeated)
+      - name: Install NESTML
+        run: |
+          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.9/site-packages
+          #echo PYTHONPATH=`pwd` >> $GITHUB_ENV
+          echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
+          python setup.py install
+
+      - name: Track Fork PR Benchmarks with Bencher
+        env:
+          LD_LIBRARY_PATH: ${{ env.NEST_INSTALL }}/lib/nest
+        run: |
+          echo "NEST_INSTALL = $NEST_INSTALL"
+          LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${{ env.NEST_INSTALL }}/lib/nest bencher run \
+          --project nestml \
+          --token '${{ secrets.BENCHER_API_TOKEN }}' \
+          --branch master \
+          --threshold-measure latency \
+          --threshold-test t_test \
+          --threshold-max-sample-size 64 \
+          --threshold-upper-boundary 0.99 \
+          --thresholds-reset \
+          --github-actions "${{ secrets.GITHUB_TOKEN }}" \
+          --testbed ubuntu-latest \
+          --adapter python_pytest \
+          --file results.json \
+          --err \
+          'LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${{ env.NEST_INSTALL }}/lib/nest python3 -m pytest --benchmark-json results.json -s $GITHUB_WORKSPACE/tests/nest_continuous_benchmarking/test_nest_continuous_benchmarking.py'
diff --git a/...hub/workflows/continuous_benchmarking.yml → ...continuous_benchmarking_pull_requests.yml b/...hub/workflows/continuous_benchmarking.yml → ...continuous_benchmarking_pull_requests.yml
@@ -23,10 +23,10 @@ jobs:
       - uses: bencherdev/bencher@main
 
       # Setup Python version
-      - name: Setup Python 3.8
+      - name: Setup Python 3.9
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       # Install dependencies
       - name: Install apt dependencies
@@ -62,7 +62,7 @@ jobs:
       # Install NESTML (repeated)
       - name: Install NESTML
         run: |
-          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.8/site-packages
+          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.9/site-packages
           #echo PYTHONPATH=`pwd` >> $GITHUB_ENV
           echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
           python setup.py install
@@ -85,87 +85,3 @@ jobs:
           --file results.json \
           --err \
           'LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${{ env.NEST_INSTALL }}/lib/nest python3 -m pytest --benchmark-json results.json -s $GITHUB_WORKSPACE/tests/nest_continuous_benchmarking/test_nest_continuous_benchmarking.py'
-
-
-on:
-  push:
-    branches: master
-
-jobs:
-  benchmark_base_branch:
-    name: Continuous Benchmarking Fork PRs with Bencher
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v4
-        with:
-          repository: ${{ github.event.pull_request.head.repo.full_name }}
-          ref: ${{ github.event.pull_request.head.sha }}
-          persist-credentials: false
-
-      - uses: bencherdev/bencher@main
-
-      # Setup Python version
-      - name: Setup Python 3.8
-        uses: actions/setup-python@v5
-        with:
-          python-version: 3.8
-
-      # Install dependencies
-      - name: Install apt dependencies
-        run: |
-          sudo apt-get update
-          sudo apt-get install libltdl7-dev libgsl0-dev libncurses5-dev libreadline6-dev pkg-config
-          sudo apt-get install python3-all-dev python3-matplotlib python3-numpy python3-scipy ipython3
-
-      # Install Python dependencies
-      - name: Python dependencies
-        run: |
-          python -m pip install --upgrade pip pytest jupyterlab matplotlib pycodestyle scipy pandas pytest-benchmark
-          python -m pip install -r requirements.txt
-
-      # Install NEST simulator
-      - name: NEST simulator
-        run: |
-          python -m pip install cython
-          echo "GITHUB_WORKSPACE = $GITHUB_WORKSPACE"
-          NEST_SIMULATOR=$(pwd)/nest-simulator
-          NEST_INSTALL=$(pwd)/nest_install
-          echo "NEST_SIMULATOR = $NEST_SIMULATOR"
-          echo "NEST_INSTALL = $NEST_INSTALL"
-
-          git clone --depth=1 https://github.com/nest/nest-simulator
-          mkdir nest_install
-          echo "NEST_INSTALL=$NEST_INSTALL" >> $GITHUB_ENV
-          cd nest_install
-          cmake -DCMAKE_INSTALL_PREFIX=$NEST_INSTALL $NEST_SIMULATOR
-          make && make install
-          cd ..
-
-      # Install NESTML (repeated)
-      - name: Install NESTML
-        run: |
-          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.8/site-packages
-          #echo PYTHONPATH=`pwd` >> $GITHUB_ENV
-          echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
-          python setup.py install
-
-      - name: Track Fork PR Benchmarks with Bencher
-        env:
-          LD_LIBRARY_PATH: ${{ env.NEST_INSTALL }}/lib/nest
-        run: |
-          echo "NEST_INSTALL = $NEST_INSTALL"
-          LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${{ env.NEST_INSTALL }}/lib/nest bencher run \
-          --project nestml \
-          --token '${{ secrets.BENCHER_API_TOKEN }}' \
-          --branch master \
-          --threshold-measure latency \
-          --threshold-test t_test \
-          --threshold-max-sample-size 64 \
-          --threshold-upper-boundary 0.99 \
-          --thresholds-reset \
-          --github-actions "${{ secrets.GITHUB_TOKEN }}" \
-          --testbed ubuntu-latest \
-          --adapter python_pytest \
-          --file results.json \
-          --err \
-          'LD_LIBRARY_PATH=$LD_LIBRARY_PATH:${{ env.NEST_INSTALL }}/lib/nest python3 -m pytest --benchmark-json results.json -s $GITHUB_WORKSPACE/tests/nest_continuous_benchmarking/test_nest_continuous_benchmarking.py'
diff --git a/.github/workflows/nestml-build.yml b/.github/workflows/nestml-build.yml
@@ -29,10 +29,10 @@ jobs:
         uses: actions/checkout@v4
 
       # Setup Python version
-      - name: Setup Python 3.8
+      - name: Setup Python 3.9
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       # Install dependencies
       - name: Install apt dependencies
@@ -60,10 +60,10 @@ jobs:
         uses: actions/checkout@v4
 
       # Setup Python version
-      - name: Setup Python 3.8
+      - name: Setup Python 3.9
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       # Install dependencies
       - name: Install apt dependencies
@@ -99,7 +99,7 @@ jobs:
       # Install NESTML
       - name: Install NESTML
         run: |
-          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.8/site-packages
+          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.9/site-packages
           #echo PYTHONPATH=`pwd` >> $GITHUB_ENV
           echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
           python setup.py install
@@ -131,10 +131,10 @@ jobs:
         uses: actions/checkout@v4
 
       # Setup Python version
-      - name: Setup Python 3.8
+      - name: Setup Python 3.9
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       # Install dependencies
       - name: Install apt dependencies
@@ -169,7 +169,7 @@ jobs:
       # Install NESTML
       - name: Install NESTML
         run: |
-          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.8/site-packages
+          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.9/site-packages
           #echo PYTHONPATH=`pwd` >> $GITHUB_ENV
           echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
           python setup.py install
@@ -195,10 +195,10 @@ jobs:
         uses: actions/checkout@v4
 
       # Setup Python version
-      - name: Setup Python 3.8
+      - name: Setup Python 3.9
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       # Install dependencies
       - name: Install apt dependencies
@@ -252,7 +252,7 @@ jobs:
       # Install NESTML (repeated)
       - name: Install NESTML
         run: |
-          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.8/site-packages
+          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.9/site-packages
           #echo PYTHONPATH=`pwd` >> $GITHUB_ENV
           echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
           python setup.py install
@@ -331,10 +331,10 @@ jobs:
         uses: actions/checkout@v4
 
       # Setup Python version
-      - name: Setup Python 3.8
+      - name: Setup Python 3.9
         uses: actions/setup-python@v5
         with:
-          python-version: 3.8
+          python-version: 3.9
 
       # Install dependencies
       - name: Install apt dependencies
@@ -370,7 +370,7 @@ jobs:
       # Install NESTML (repeated)
       - name: Install NESTML
         run: |
-          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.8/site-packages
+          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.9/site-packages
           #echo PYTHONPATH=`pwd` >> $GITHUB_ENV
           echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
           python setup.py install

diff --git a/doc/installation.rst b/doc/installation.rst
@@ -1,7 +1,7 @@
 Installing NESTML
 =================
 
-Please note that only Python 3.8 (and later versions) are supported. The instructions below assume that ``python`` is aliased to or refers to ``python3``, and ``pip`` to ``pip3``.
+Please note that only Python 3.9 (and later versions) are supported. The instructions below assume that ``python`` is aliased to or refers to ``python3``, and ``pip`` to ``pip3``.
 
 Installing the latest release from PyPI
 ---------------------------------------

diff --git a/setup.py b/setup.py
@@ -23,7 +23,7 @@
 import sys
 from setuptools import setup, find_packages
 
-assert sys.version_info.major >= 3 and sys.version_info.minor >= 8, "Python 3.8 or higher is required to run NESTML"
+assert sys.version_info.major >= 3 and sys.version_info.minor >= 9, "Python 3.9 or higher is required to run NESTML"
 
 with open("requirements.txt") as f:
     requirements = f.read().splitlines()