Merge branch 'master' into 1uc/modernize-something

neuronsimulator · Jan 15, 2025 · a7d777a · a7d777a
2 parents fbfecb2 + 74dcdd5
commit a7d777a
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Showing 55 changed files with 486 additions and 945 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -1,13 +1,13 @@
 version: 2.1
 
 orbs:
-  python: circleci/python@2.1.1
+  python: circleci/python@3.0.0
 
 jobs:
   manylinux2014-aarch64:
 
     parameters:
-      NRN_PYTHON_VERSION:
+      NRN_PYTHON_VERSION_MINOR:
         type: string
       NRN_NIGHTLY_UPLOAD:
         type: string
@@ -31,8 +31,8 @@ jobs:
                 -e NRN_RELEASE_UPLOAD \
                 -e SETUPTOOLS_SCM_PRETEND_VERSION \
                 -e NRN_BUILD_FOR_UPLOAD=1 \
-                'neuronsimulator/neuron_wheel:latest-gcc9-aarch64' \
-                packaging/python/build_wheels.bash linux << parameters.NRN_PYTHON_VERSION >> coreneuron
+                'neuronsimulator/neuron_wheel:latest-aarch64' \
+                packaging/python/build_wheels.bash linux 3<< parameters.NRN_PYTHON_VERSION_MINOR >> coreneuron
 
       - store_artifacts:
           path: ./wheelhouse
@@ -41,24 +41,17 @@ jobs:
       - run:
           name: Test manylinux AArch64 wheel
           command: |
-
-            # install mpi dependencies
+            sudo apt purge -y needrestart
+            sudo apt update
+            echo "deb http://ppa.launchpad.net/deadsnakes/ppa/ubuntu jammy main" | sudo tee /etc/apt/sources.list.d/deadsnakes-ppa.list && sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys F23C5A6CF475977595C89F51BA6932366A755776 && sudo apt update
             sudo apt update
+            # install mpi dependencies
             sudo apt install -y mpich openmpi-bin libopenmpi-dev libmpich-dev
+            version=3.<< parameters.NRN_PYTHON_VERSION_MINOR >>
+            # install Python from deadsnakes
+            sudo apt install -y python${version}-venv libpython${version}-dev g++ make
 
-            # choose available python versions from pyenv
-            pyenv_py_ver=""
-            case << parameters.NRN_PYTHON_VERSION >> in
-              39) pyenv_py_ver="3.9" ;;
-              310) pyenv_py_ver="3.10" ;;
-              311) pyenv_py_ver="3.11" ;;
-              312) pyenv_py_ver="3.12" ;;
-              *) echo "Error: pyenv python version not specified or not supported." && exit 1;;
-            esac
-
-            env PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install $pyenv_py_ver --force
-            pyenv global $pyenv_py_ver
-            export PYTHON_EXE=$(which python)
+            export PYTHON_EXE=$(which python3.<< parameters.NRN_PYTHON_VERSION_MINOR >>)
 
             # test wheel
             packaging/python/test_wheels.sh $PYTHON_EXE $(ls -t wheelhouse/*.whl)
@@ -86,7 +79,7 @@ workflows:
                 - /circleci\/.*/
           matrix:
             parameters:
-              NRN_PYTHON_VERSION: ["312"]
+              NRN_PYTHON_VERSION_MINOR: ["13"]
               NRN_NIGHTLY_UPLOAD: ["false"]
 
   nightly:
@@ -101,5 +94,5 @@ workflows:
       - manylinux2014-aarch64:
           matrix:
             parameters:
-              NRN_PYTHON_VERSION: ["39", "310", "311", "312"]
+              NRN_PYTHON_VERSION_MINOR: ["9", "10", "11", "12", "13"]
               NRN_NIGHTLY_UPLOAD: ["true"]
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -24,7 +24,7 @@ on:
 env:
   PY_MIN_VERSION: '3.9'
   PY_MID_VERSION: '3.10'
-  PY_MAX_VERSION: '3.12'
+  PY_MAX_VERSION: '3.13'
 
 jobs:
   coverage:

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -17,7 +17,7 @@ on:
       - release/**
 
 env:
-  DEFAULT_PY_VERSION: '3.12'
+  DEFAULT_PY_VERSION: '3.13'
 
 jobs:
   documentation:

diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
@@ -39,7 +39,7 @@ jobs:
       DESIRED_CMAKE_VERSION: 3.17
       DYNAMIC_PYTHON_CMAKE_VERSION: 3.18
       PY_MIN_VERSION: ${{ matrix.config.python_min_version || '3.9' }}
-      PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.12' }}
+      PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.13' }}
       MUSIC_INSTALL_DIR: /opt/MUSIC
       # hash of commit containing mpi4py 4 fix
       MUSIC_VERSION: '13f312338dcccebfe74d391b1b24f1b6d816ac6c'
@@ -125,6 +125,8 @@ jobs:
             brew install cmake
             echo "$(brew --prefix)/opt/cmake/bin" >> $GITHUB_PATH
           fi
+          # workaround for fmt 11.1 (see https://github.com/gabime/spdlog/pull/3312)
+          brew unlink fmt
           echo "$(brew --prefix)/opt/flex/bin:$(brew --prefix)/opt/bison/bin" >> $GITHUB_PATH
           # Core https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners/about-github-hosted-runners#standard-github-hosted-runners-for-public-repositories
           if [[ "${{matrix.os}}" == "macOS-13" ]]; then