NEURON 8.0.1 release

.github/workflows/coverage.yml

@@ -14,6 +14,10 @@ on:
       - '**.rst'
       - 'docs/**'
 
+env:
+  PY_MIN_VERSION: 2.7
+  PY_MAX_VERSION: 3.8
+
 jobs:
   coverage:
     runs-on: ubuntu-18.04
@@ -29,22 +33,24 @@ jobs:
           sudo apt-get install  build-essential doxygen autoconf automake libtool lcov autotools-dev libopenmpi-dev libmpich-dev libx11-dev libxcomposite-dev mpich openmpi-bin patchelf python-pip python-tk python-numpy python3-numpy python3-pip g++-5 g++-6 g++-8 g++-9
         shell: bash
 
-      - name: Set up Python2
+      - name: Set up Python@${{ env.PY_MIN_VERSION }}
         uses: actions/setup-python@v2
         with:
-          python-version: '2.x'
+          python-version: ${{ env.PY_MIN_VERSION }}
 
-      - name: Set up Python3
+      - name: Set up Python@${{ env.PY_MAX_VERSION }}
         uses: actions/setup-python@v2
         with:
-          python-version: '3.8'
-
-      - name: Install Python3 dependencies
-        run: python3 -m pip install --upgrade pip wheel setuptools scikit-build pytest matplotlib bokeh ipython cython pytest pytest-cov mpi4py
+          python-version: ${{ env.PY_MAX_VERSION }}
 
       - uses: actions/checkout@v2
         with:
-           fetch-depth: 2
+          fetch-depth: 2
+
+      - name: Install Python@${{ env.PY_MAX_VERSION }} dependencies
+        working-directory: ${{runner.workspace}}/nrn
+        run: |
+          python -m pip install --upgrade pip -r nrn_requirements.txt
 
       - name: Build & Test
         id: build-test
@@ -58,14 +64,14 @@ jobs:
           export CXX=g++
 
           # Python setup
-          export PYTHON2=$(which python2);
-          export PYTHON3=$(which python3);
+          export PYTHON_MIN=$(which $PYTHON_MIN_NAME);
+          export PYTHON_MAX=$(which $PYTHON_MAX_NAME);
 
           mkdir build && cd build;
 
           # CMake options & flags
           export COVERAGE_FLAGS="--coverage -O0 -fno-inline -g";
-          export CMAKE_OPTION="-DNRN_ENABLE_BINARY_SPECIAL=ON -DNRN_ENABLE_MPI=ON -DNRN_ENABLE_INTERVIEWS=ON -DNRN_ENABLE_PYTHON=ON -DNRN_ENABLE_PYTHON_DYNAMIC=ON -DNRN_PYTHON_DYNAMIC=${PYTHON2};${PYTHON3} -DNRN_ENABLE_CORENEURON=ON";
+          export CMAKE_OPTION="-DNRN_ENABLE_BINARY_SPECIAL=ON -DNRN_ENABLE_MPI=ON -DNRN_ENABLE_INTERVIEWS=ON -DNRN_ENABLE_PYTHON=ON -DNRN_ENABLE_PYTHON_DYNAMIC=ON -DNRN_PYTHON_DYNAMIC=${PYTHON_MIN};${PYTHON_MAX} -DNRN_ENABLE_CORENEURON=ON";
           cmake $CMAKE_OPTION -DCMAKE_C_COMPILER=$CC -DCMAKE_CXX_COMPILER=$CXX -DNRN_ENABLE_TESTS=ON -DCMAKE_C_FLAGS="${COVERAGE_FLAGS}" -DCMAKE_CXX_FLAGS="${COVERAGE_FLAGS}" ..;
 
           # Coverage
@@ -82,6 +88,8 @@ jobs:
           bash <(curl -s https://codecov.io/bash)
         env:
           MATRIX_EVAL: "CC=gcc CXX=g++"
+          PYTHON_MIN_NAME: "python${{ env.PY_MIN_VERSION }}"
+          PYTHON_MAX_NAME: "python${{ env.PY_MAX_VERSION }}"
 
       # This step will set up an SSH connection on tmate.io for live debugging.
       # To trigger it, simply add 'live-debug-coverage' to your last pushed commit message.

.github/workflows/docs.yml

@@ -10,6 +10,9 @@ on:
       - master
       - release/**
 
+env:
+  DEFAULT_PY_VERSION: 3.8
+
 jobs:
   documentation:
     runs-on: ubuntu-18.04
@@ -22,39 +25,39 @@ jobs:
 
       - name: Install apt packages
         run: |
-          sudo apt-get update && sudo apt-get upgrade
-          sudo apt-get install build-essential autoconf automake libtool autotools-dev libopenmpi-dev libmpich-dev libx11-dev libxcomposite-dev mpich openmpi-bin patchelf python-pip python-tk python-numpy python3-numpy python3-pip g++-5 g++-6 g++-8 g++-9
+          sudo apt-get install build-essential autoconf automake libtool autotools-dev libopenmpi-dev libmpich-dev libx11-dev libxcomposite-dev mpich openmpi-bin patchelf g++-5 g++-6 g++-8 g++-9
           sudo apt-get install ffmpeg doxygen
         shell: bash
 
-      - name: Set up Python3
+      - name: Set up Python@${{ env.DEFAULT_PY_VERSION }}
         uses: actions/setup-python@v2
         with:
-          python-version: '3.8'
+          python-version: ${{ env.DEFAULT_PY_VERSION }}
+
+      - uses: actions/checkout@v2
 
-      - name: Install Python3 dependencies
+      - name: Install Python dependencies
         working-directory: ${{runner.workspace}}/nrn
         run: |
-          python3 -m pip install --upgrade pip wheel setuptools scikit-build pytest matplotlib bokeh ipython cython pytest pytest-cov mpi4py
+          python -m pip install --upgrade pip -r nrn_requirements.txt
 
-      - uses: actions/checkout@v2
-
-      - name: Install Python3 documentation dependencies
+      - name: Install Python documentation dependencies
         working-directory: ${{runner.workspace}}/nrn
-        run: python3 -m pip install --upgrade -r docs/docs_requirements.txt
+        run: |
+          python -m pip install --upgrade -r docs/docs_requirements.txt
 
       - name: Documentation
         id: documentation
         shell: bash
         working-directory: ${{runner.workspace}}/nrn
         run:  |
           echo "-------- NEURON wheel --------";
-          python3 setup.py build_ext bdist_wheel;
+          python setup.py build_ext bdist_wheel;
           neuron_wheel=dist/NEURON*.whl;
           echo "-------- install wheel --------"
-          python3 -m pip install $neuron_wheel;
+          python -m pip install $neuron_wheel;
           echo "-------- now build docs--------";
-          python3 setup.py docs;
+          python setup.py docs;
           echo "-------- disable jekyll--------";
           pushd docs/_build;
           touch .nojekyll;

.github/workflows/neuron-ci.yml

@@ -19,6 +19,7 @@ env:
   BUILD_TYPE: Release
   DEVELOPER_DIR: /Applications/Xcode_11.3.1.app/Contents/Developer
   DESIRED_CMAKE_VERSION: 3.8.2
+  DEFAULT_PY_VERSION: 3.8
 
 jobs:
   ci:
@@ -65,24 +66,28 @@ jobs:
           sudo apt-get install build-essential autoconf automake libtool autotools-dev libopenmpi-dev libmpich-dev libx11-dev libxcomposite-dev mpich openmpi-bin patchelf python-pip python-tk python-numpy python3-numpy python3-pip g++-5 g++-6 g++-8 g++-9
         shell: bash
 
+      - uses: actions/checkout@v2
+
       - name: Set up Python2
         uses: actions/setup-python@v2
         with:
           python-version: '2.x'
 
       - name: Install Python2 dependencies
         if: ${{ matrix.config.use_python2 == 'ON' || matrix.config.python_dynamic == 'ON' }}
-        run: python2 -m pip install --upgrade pip wheel setuptools scikit-build pytest matplotlib bokeh ipython cython pytest pytest-cov mpi4py pathlib
+        working-directory: ${{runner.workspace}}/nrn
+        run: |
+          python2 -m pip install --upgrade pip pathlib -r nrn_requirements.txt
 
-      - name: Set up Python3
+      - name: Set up Python@${{ env.DEFAULT_PY_VERSION }}
         uses: actions/setup-python@v2
         with:
-          python-version: '3.8'
+          python-version: ${{ env.DEFAULT_PY_VERSION }}
 
-      - name: Install Python3 dependencies
-        run: python3 -m pip install --upgrade pip wheel setuptools scikit-build pytest matplotlib bokeh ipython cython pytest pytest-cov mpi4py
-
-      - uses: actions/checkout@v2
+      - name: Install Python@${{ env.DEFAULT_PY_VERSION }} dependencies
+        working-directory: ${{runner.workspace}}/nrn
+        run: |
+          python -m pip install --upgrade pip -r nrn_requirements.txt
 
       - name: Build and Test
         id: build-test

.github/workflows/windows.yml

@@ -59,7 +59,14 @@ jobs:
         name: nrn-nightly-AMD64.exe
         path: ${{runner.workspace}}\nrn\nrn-nightly-AMD64.exe
 
+    - name: Run installer and launch .hoc associaton test
+      run: .\ci\win_install_neuron.cmd
+      shell: cmd
+      working-directory: ${{runner.workspace}}\nrn
+
     - name: Test Installer
-      run: .\ci\win_test_installer.cmd
+      # temporarily disable rxd testing ( ci/win_test_installer.cmd <-> ci/win_test_installer_wo_rxd.cmd)
+      # see https://github.com/neuronsimulator/nrn/issues/1522
+      run: .\ci\win_test_installer_wo_rxd.cmd
       shell: cmd
       working-directory: ${{runner.workspace}}\nrn

CMakeLists.txt

@@ -553,8 +553,13 @@ if(NRN_ENABLE_TESTS)
   include(CTest)
   include(Catch)
   find_python_module(pytest)
-  if(NRN_ENABLE_PYTHON AND NOT PYTEST_FOUND)
-    message(SEND_ERROR "pytest Python package is required.")
+  find_python_module(pytest_cov)
+  if(NRN_ENABLE_PYTHON)
+    if(NOT PYTEST_FOUND)
+      message(SEND_ERROR "pytest Python package is required.")
+    elseif(NOT PYTEST_COV_FOUND)
+      message(WARNING "pytest-cov package not installed. Python coverage will not be generated.")
+    endif()
   endif()
   # Initialize the submodule *before* including the test/CMakeLists.txt that uses it. This ensures
   # that the test infrastructure can find the names of the input data files and set up rules to copy

azure-pipelines.yml

@@ -26,7 +26,7 @@ trigger:
 
 jobs:
 
-- job: 'ManyLinuxWheels'
+- job: 'ManyLinux1Wheels'
   timeoutInMinutes: 30
   pool:
     vmImage: 'ubuntu-18.04'
@@ -54,7 +54,7 @@ jobs:
         -e NRN_RELEASE_UPLOAD \
         -e NEURON_WHEEL_VERSION \
         -e NRN_BUILD_FOR_UPLOAD=1 \
-        'neuronsimulator/neuron_wheel' \
+        'neuronsimulator/neuron_wheel:manylinux1' \
         packaging/python/build_wheels.bash linux $(python.version)
     displayName: 'Building ManyLinux Wheel'
 
@@ -66,6 +66,35 @@ jobs:
   - template: ci/azure-wheel-test-upload.yml
 
 
+- job: 'ManyLinux2014Wheels'
+  timeoutInMinutes: 30
+  pool:
+    vmImage: 'ubuntu-18.04'
+  strategy:
+    matrix:
+      Python310:
+        python.version: '3.10'
+  steps:
+    - script: |
+        docker run --rm \
+          -w /root/nrn \
+          -v $PWD:/root/nrn \
+          -e NEURON_NIGHTLY_TAG \
+          -e NRN_NIGHTLY_UPLOAD \
+          -e NRN_RELEASE_UPLOAD \
+          -e NEURON_WHEEL_VERSION \
+          -e NRN_BUILD_FOR_UPLOAD=1 \
+          'neuronsimulator/neuron_wheel:latest' \
+          packaging/python/build_wheels.bash linux $(python.version)
+      displayName: 'Building ManyLinux Wheel'
+
+    - script: |
+        sudo apt update
+        sudo apt install -y mpich openmpi-bin libopenmpi-dev libmpich-dev
+      displayName: 'Install Test System Depdendencies'
+
+    - template: ci/azure-wheel-test-upload.yml
+
 # Jobs to build OSX wheels natively
 - job: 'MacOSWheels'
   timeoutInMinutes: 30
@@ -76,29 +105,36 @@ jobs:
       Python27:
         python.version: '2.7'
         python.org.version: '2.7.18'
+        python.installer.name: 'macosx10.9.pkg'
       Python35:
         python.version: '3.5'
         python.org.version: '3.5.4'
+        python.installer.name: 'macosx10.6.pkg'
       Python36:
         python.version: '3.6'
         python.org.version: '3.6.8'
+        python.installer.name: 'macosx10.9.pkg'
       Python37:
         python.version: '3.7'
         python.org.version: '3.7.7'
+        python.installer.name: 'macosx10.9.pkg'
       Python38:
         python.version: '3.8'
         python.org.version: '3.8.2'
+        python.installer.name: 'macosx10.9.pkg'
       Python39:
         python.version: '3.9'
         python.org.version: '3.9.0'
+        python.installer.name: 'macosx10.9.pkg'
+      Python310:
+        python.version: '3.10'
+        python.org.version: '3.10.0'
+        python.installer.name: 'macos11.pkg'
+
   steps:
 
   - script: |
-      if [ "$(python.org.version)" == "3.5.4" ]; then
-        installer=python-$(python.org.version)-macosx10.6.pkg
-      else
-        installer=python-$(python.org.version)-macosx10.9.pkg
-      fi
+      installer=python-$(python.org.version)-$(python.installer.name)
       url=https://www.python.org/ftp/python/$(python.org.version)/$installer
       curl $url -o $installer
       sudo installer -pkg $installer -target /

ci/association.hoc

@@ -0,0 +1,11 @@
+objref f
+f = new File()
+if (f.ropen("association.hoc.out")) {
+  f.close()
+  f.unlink()
+}
+f.wopen("association.hoc.out")
+f.printf("%s\n","hello")
+f.flush()
+f.close()
+quit()

ci/azure-wheel-test-upload.yml

@@ -12,6 +12,7 @@ steps:
     displayName: 'Test with brew Python'
 
   - task: UsePythonVersion@0
+    condition: ne(variables['python.version'], '3.5')
     inputs:
       versionSpec: '$(python.version)'
 
@@ -20,6 +21,7 @@ steps:
       # note : python2 has two wheels cp27m and cp27mu (unicode). cp27mu is built last
       # and this is what compatible for testing on azure host.
       packaging/python/test_wheels.sh $(which python) $(ls -t wheelhouse/*.whl)
+    condition: ne(variables['python.version'], '3.5')
     displayName: 'Test with System Python'
 
   - task: TwineAuthenticate@1

ci/azure-win-installer-upload.yml

@@ -10,13 +10,17 @@ steps:
       versionSpec: '2.7'
     displayName: "Use System Python"
 
-# Note: silently installing neuron doesn't work, when we print out the contents of the installation folder not all files
-# are there. We suspect an Azure issue since we've tried a lot of things (to name a few: trying NSIS 3.04 commit that
-# was working back then, changing NSIS installers, trying latest NSIS, different process waiting strategies including
-# powershell and start /wait and so on) and locally testing the installer works.
   - task: BatchScript@1
     inputs:
-      filename: ci/win_test_installer.cmd
+      filename: ci/win_install_neuron.cmd
+    displayName: "Run Installer and launch .hoc association test"
+    condition: succeeded()
+
+  - task: BatchScript@1
+    inputs:
+      # temporarily disable rxd testing ( ci/win_test_installer.cmd <-> ci/win_test_installer_wo_rxd.cmd)
+      # see https://github.com/neuronsimulator/nrn/issues/1522
+      filename: ci/win_test_installer_wo_rxd.cmd
     displayName: "Test Installer"
     condition: succeeded()
 

ci/win_build_cmake.sh

@@ -24,7 +24,7 @@ cd $BUILD_SOURCESDIRECTORY/build
 	-DNRN_RX3D_OPT_LEVEL=2 \
 	-DPYTHON_EXECUTABLE=/c/Python35/python.exe \
 	-DNRN_ENABLE_PYTHON_DYNAMIC=ON  \
-	-DNRN_PYTHON_DYNAMIC='c:/Python35/python.exe;c:/Python36/python.exe;c:/Python37/python.exe;c:/Python38/python.exe;c:/Python39/python.exe;c:/Python27/python.exe'  \
+	-DNRN_PYTHON_DYNAMIC='c:/Python35/python.exe;c:/Python36/python.exe;c:/Python37/python.exe;c:/Python38/python.exe;c:/Python39/python.exe;c:/Python27/python.exe;c:/Python310/python.exe'  \
 	-DCMAKE_INSTALL_PREFIX='/c/nrn-install' \
 	-DMPI_CXX_LIB_NAMES:STRING=msmpi \
 	-DMPI_C_LIB_NAMES:STRING=msmpi \

ci/win_download_deps.cmd

@@ -9,13 +9,14 @@ pwsh -command Invoke-WebRequest -MaximumRetryCount 4 -OutFile python-3.7.exe htt
 pwsh -command Invoke-WebRequest -MaximumRetryCount 4 -OutFile python-3.8.exe https://www.python.org/ftp/python/3.8.2/python-3.8.2-amd64.exe || goto :error
 pwsh -command Invoke-WebRequest -MaximumRetryCount 4 -OutFile python-3.9.exe https://www.python.org/ftp/python/3.9.0/python-3.9.0-amd64.exe || goto :error
 pwsh -command Invoke-WebRequest -MaximumRetryCount 4 -OutFile python-2.7.msi https://www.python.org/ftp/python/2.7.17/python-2.7.17.amd64.msi || goto :error
+pwsh -command Invoke-WebRequest -MaximumRetryCount 4 -OutFile python-3.10.exe https://www.python.org/ftp/python/3.10.0/python-3.10.0-amd64.exe || goto :error
 
 :: mpi
 pwsh -command Invoke-WebRequest -MaximumRetryCount 4 -OutFile msmpisetup.exe https://download.microsoft.com/download/a/5/2/a5207ca5-1203-491a-8fb8-906fd68ae623/msmpisetup.exe || goto :error
 pwsh -command Invoke-WebRequest -MaximumRetryCount 4 -OutFile msmpisdk.msi https://download.microsoft.com/download/a/5/2/a5207ca5-1203-491a-8fb8-906fd68ae623/msmpisdk.msi || goto :error
 
 :: nsis + plugin
-curl -LO --retry 4 http://prdownloads.sourceforge.net/nsis/nsis-3.05-setup.exe
+curl -LO --retry 4 http://prdownloads.sourceforge.net/nsis/nsis-3.05-setup.exe || goto :error
 pwsh -command Invoke-WebRequest -MaximumRetryCount 4 -OutFile EnVar_pugin.zip https://nsis.sourceforge.io/mediawiki/images/7/7f/EnVar_plugin.zip || goto :error
 
 :: if all goes well, go to end