Hines/fix 8.2.2

.github/workflows/docs.yml

@@ -23,23 +23,25 @@ jobs:
 
     name: Documentation
 
-    timeout-minutes: 20
+    timeout-minutes: 25
 
     steps:
 
       - name: Install apt packages
         run: |
           sudo apt-get update --fix-missing
-          sudo apt-get install build-essential libopenmpi-dev libmpich-dev libx11-dev libxcomposite-dev mpich openmpi-bin patchelf
+          sudo apt-get install build-essential libopenmpi-dev libmpich-dev libx11-dev libxcomposite-dev mpich openmpi-bin
           sudo apt-get install ffmpeg doxygen pandoc
         shell: bash
 
       - name: Set up Python@${{ env.DEFAULT_PY_VERSION }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ env.DEFAULT_PY_VERSION }}
 
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
 
       - name: Install Python dependencies
         working-directory: ${{runner.workspace}}/nrn
@@ -67,7 +69,7 @@ jobs:
           pushd docs/_build;
           touch .nojekyll;
           echo "-------- OK to deploy! --------";
-          echo ::set-output name=status::done;
+          echo "OK_TO_DEPLOY_DOCS=true" >> $GITHUB_ENV
 
       # This step will set up an SSH connection on tmate.io for live debugging.
       # To enable it, you have to:
@@ -78,8 +80,8 @@ jobs:
         uses: mxschmitt/action-tmate@v3
 
       - name: Deploy 🚀
-        uses: JamesIves/github-pages-deploy-action@4.1.5
-        if: steps.documentation.outputs.status == 'done' && github.ref == 'refs/heads/master'
+        uses: JamesIves/github-pages-deploy-action@v4
+        if: env.OK_TO_DEPLOY_DOCS == 'true' && github.ref == 'refs/heads/master'
         with:
           branch: gh-pages # The branch the action should deploy to.
           folder: ${{runner.workspace}}/nrn/docs/_build # The folder the action should deploy.

.github/workflows/formatting.yml

@@ -28,7 +28,7 @@ jobs:
       - name: Install Black
         run: |
           python -m pip install --upgrade pip
-          python -m pip install --upgrade black[jupyter]
+          python -m pip install --upgrade black[jupyter]==22.12.0
 
       - uses: actions/checkout@v3
 

CMakeLists.txt

@@ -17,7 +17,7 @@ if(DEFINED ENV{CRAYPE_VERSION})
 endif()
 project(
   NEURON
-  VERSION 8.2.2
+  VERSION 8.2.3
   LANGUAGES C CXX
   HOMEPAGE_URL "https://www.neuron.yale.edu/neuron/")
 

azure-pipelines.yml

@@ -80,61 +80,6 @@ stages:
 
       - template: ci/azure-wheel-test-upload.yml
 
-
-    - job: 'ManyLinuxGPUWheels'
-      timeoutInMinutes: 30
-      pool:
-        vmImage: 'ubuntu-20.04'
-      variables:
-        GPU_BUILD: 'true'
-      strategy:
-        matrix:
-          Python37:
-            python.version: '3.7'
-          Python38:
-            python.version: '3.8'
-          Python39:
-            python.version: '3.9'
-          Python310:
-            python.version: '3.10'
-          Python311:
-            python.version: '3.11'
-      steps:
-
-      # Secure files documentation:
-      #   https://docs.microsoft.com/en-us/azure/devops/pipelines/library/secure-files?view=azure-devops
-      #   NOTE: when uploading new secure files, access must be permitted from the Azure pipeline interface (check message there)
-      - task: DownloadSecureFile@1
-        name: mpt_headersSF
-        displayName: 'Download mpt_headers secure file'
-        inputs:
-          secureFile: 'mpt_headears.2.21.tar.gz'
-
-      # Note that mpt headers must be mounted in the docker imager under `/nrnwheel/mpt`
-      # This path is checked by `packaging/python/build_wheels.bash` when run in the image.
-      - script: |
-          sudo mkdir -p /opt/nrnwheel/mpt
-          sudo tar -zxf $(mpt_headersSF.secureFilePath) --directory /opt/nrnwheel/mpt
-          docker run --rm \
-            -w /root/nrn \
-            -v $PWD:/root/nrn \
-            -v /opt/nrnwheel/mpt:/nrnwheel/mpt \
-            -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_gpu:nvhpc-22.1-cuda-11.5' \
-            packaging/python/build_wheels.bash linux $(python.version) coreneuron-gpu
-        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: 40
@@ -192,7 +137,7 @@ stages:
         name: readlineSF
         displayName: 'Download readline secure file'
         inputs:
-          secureFile: 'readline7.0.tar.gz'
+          secureFile: 'readline7.0-ncurses6.4.tar.gz'
 
       - script: |
           export MACOSX_DEPLOYMENT_TARGET=10.9

docs/conda_environment.yml

@@ -8,7 +8,7 @@ dependencies:
   - cmake
   - xorg-libxcomposite
   - ffmpeg
-  - cython
+  - cython<3
   - pandoc
   - pip
   - pip: