Merge branch 'master' into docs/project-management

.bbp-project.yaml

@@ -0,0 +1,14 @@
+tools:
+  Black:
+    enable: True
+    include:
+      match:
+      - '.*\.(py|ipynb)$'
+    option: [--color, --target-version, py37]
+    version: '[jupyter] ~=22.3'
+  ClangFormat:
+    enable: True
+    version: == 12.0.1
+  CMakeFormat:
+    enable: True
+    version: == 0.6.13

.circleci/config.yml

@@ -0,0 +1,107 @@
+version: 2.1
+
+orbs:
+  python: circleci/[email protected]
+
+jobs:
+  manylinux2014-aarch64:
+
+    parameters:
+      NRN_PYTHON_VERSION:
+        type: string
+      NRN_NIGHTLY_UPLOAD:
+        type: string
+
+    machine:
+      image: default
+
+    resource_class: arm.medium
+
+    steps:
+      - checkout
+      - run:
+          name: Build manylinux AArch64 wheel
+          command: |
+            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 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
+
+      - store_artifacts:
+          path: ./wheelhouse
+          destination: artifacts
+
+      - run:
+          name: Test manylinux AArch64 wheel
+          command: |
+
+            # install mpi dependencies
+            sudo apt update
+            sudo apt install -y mpich openmpi-bin libopenmpi-dev libmpich-dev
+
+            # choose available python versions from pyenv
+            pyenv_py_ver=""
+            case << parameters.NRN_PYTHON_VERSION >> in
+              38) pyenv_py_ver="3.8" ;;
+              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!" && exit 1;;
+            esac
+
+            cd /opt/circleci/.pyenv/plugins/python-build/../.. && git fetch --all && git checkout -B master origin/master && cd -
+            env PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install $pyenv_py_ver --force
+            pyenv global $pyenv_py_ver
+            export PYTHON_EXE=$(which python)
+
+            # test wheel
+            packaging/python/test_wheels.sh $PYTHON_EXE $(ls -t wheelhouse/*.whl)
+
+      - run:
+          name: Upload nightly wheel to pypi.org
+          command: |
+            if [ "<< parameters.NRN_NIGHTLY_UPLOAD >>" == "true" ]; then
+              python -m pip install --upgrade pip
+              python -m pip install twine
+              python -m twine upload --verbose --skip-existing -u $TWINE_USERNAME -p $TWINE_PASSWORD  wheelhouse/*.whl
+            else
+              echo "Skipping pypi.org upload!"
+            fi
+
+workflows:
+
+  build-workflow:
+    jobs:
+      - manylinux2014-aarch64:
+          filters:
+            branches:
+              only:
+                - /release\/.*/
+                - /circleci\/.*/
+          matrix:
+            parameters:
+              NRN_PYTHON_VERSION: ["312"]
+              NRN_NIGHTLY_UPLOAD: ["false"]
+
+  nightly:
+    triggers:
+      - schedule:
+          cron: "0 0 * * *"
+          filters:
+            branches:
+              only:
+                - master
+    jobs:
+      - manylinux2014-aarch64:
+          matrix:
+            parameters:
+              NRN_PYTHON_VERSION: ["38", "39", "310", "311", "312"]
+              NRN_NIGHTLY_UPLOAD: ["true"]

.clang-format.changes

@@ -1,2 +1,11 @@
 SortIncludes: false
-Standard: Cpp03
+Standard: c++17
+StatementMacros: [MKDLL, MKDLLdec, MKDLLif, MKDLLvp, MKDLLvpf, MUTDEC, PyObject_HEAD,
+declareActionCallback, declareAdjustStepper, declareArrowGlyph, declareFieldEditorCallback,
+declareFieldSEditorCallback, declareFileChooserCallback, declareIOCallback, declareList, 
+declarePtrList, declareRubberCallback, declareSelectionCallback, declareTable, declareTable2,
+HocContextRestore, HocTopContextSet,
+implementActionCallback, implementAdjustStepper, implementArrowGlyph, implementFieldEditorCallback,
+implementFieldSEditorCallback, implementFileChooserCallback, implementIOCallback, implementList,
+implementPtrList, implementRubberCallback, implementSelectionCallback, implementTable,
+implementTable2, nrn_pragma_acc, nrn_pragma_omp, TBUF]

.cmake-format.changes.yaml

@@ -2,25 +2,30 @@ additional_commands:
   nrn_add_test_group:
     pargs: 0
     kwargs:
+      CORENEURON: 0
+      ENVIRONMENT: '+'
       NAME: 1
-      SUBMODULE: '?'
-      MODFILE_PATTERNS: '*'
-      SCRIPT_PATTERNS: '*'
-      OUTPUT: '*'
+      MODFILE_PATTERNS: '+'
+      NRNIVMODL_ARGS: '+'
+      OUTPUT: '+'
+      SCRIPT_PATTERNS: '+'
+      SIM_DIRECTORY: 1
+      SUBMODULE: 1
   nrn_add_test:
     pargs: 0
     kwargs:
       GROUP: 1
       NAME: 1
-      SUBMODULE: '?'
-      MODFILE_PATTERNS: '*'
-      PRECOMMAND: '+'
       COMMAND: '+'
-      SCRIPT_PATTERNS: '*'
-      REQUIRES: '*'
-      CONFLICTS: '*'
+      ENVIRONMENT: '+'
+      CONFLICTS: '+'
+      PRECOMMAND: '+'
+      PRELOAD_SANITIZER: 0
+      PROCESSORS: 1
+      REQUIRES: '+'
       OUTPUT: '*'
-      PROCESSORS: '?'
+      SCRIPT_PATTERNS: '*'
+      SIM_DIRECTORY: '?'
   nrn_add_test_group_comparison:
     pargs: 0
     kwargs:

.git-blame-ignore-revs

@@ -1,2 +1,10 @@
 # Ignore blame of black formatting
 4c6fd585f2d6138db5f77513a795a53cc56b0646
+# Ignore blame of black formatting fixup #1729
+d65a7083dbc54bede71aaf37c91677c8ce1f089d
+# Ignore blame of cmake-format formatting #1730
+c5d0fc9499c22b947d76b65dfa756be154b93f18
+# Ignore blame of clang-format formatting #1732
+013b69a92bcbd09d917e5519940f75c511ed5072
+# Ignore blame of extra clang-format formatting #1748
+4d9a02539d13636c8e27cc123846072837d760be

.github/ISSUE_TEMPLATE/release-patch.md

@@ -0,0 +1,96 @@
+---
+name: NEURON Patch Release
+about: Create a NEURON Patch release for an existing branch.
+title: 'NEURON [x.y.z] patch release'
+labels: 'release'
+assignees: ''
+
+---
+
+Action items
+============
+
+Pre-release
+---
+- [ ] Create a cherrypicks branch where all commits go into new release and open a PR against `release/x.y` branch
+- [ ] Make sure to look out for ModelDB regressions by manually submitting and analyzing [nrn-modeldb-ci](https://github.com/neuronsimulator/nrn-modeldb-ci/actions/workflows/nrn-modeldb-ci.yaml?query=event%3Aschedule++) for the cherrypicks branch vs previous version
+- [ ] Update cherrypicks PR:
+  - [ ] Update semantic version in `CMakeLists.txt`
+  - [ ] Update changelog below and agree on it with everyone; then commit it to `docs/changelog` in the cherrypicks PR (copy structure as-is)
+  - [ ] Update `docs/index.rst` accordingly with the new `.pkg` and `.exe` links for `PKG installer` and `Windows Installer`
+
+Sanity checks
+---
+- [ ] After cherrypicks PR is merged, make sure GitHub, Azure and CircleCI builds pass for `release/x.y` branch
+- [ ] Run [nrn-build-ci](https://github.com/neuronsimulator/nrn-build-ci/actions/workflows/build-neuron.yml) for the `release/x.y` branch; see [nrn-build-ci guide](https://github.com/neuronsimulator/nrn-build-ci#azure-wheels-testing---manual-workflow)
+- [ ] Activate ReadTheDocs build for `release/x.y` & make it hidden. Check docs are fine after build is done.
+- [ ] Run BBP Simulation Stack & other relevant tests
+
+
+Releasing
+---
+- [ ] Create new release+tag on GitHub via [release workflow](https://github.com/neuronsimulator/nrn/actions/workflows/release.yml?query=workflow%3A%22NEURON+Release%22). Note that the GitHub release will be marked as pre-release and  will contain the full-src-package and the Windows installer at the end of the release workflow.
+- [ ] Build release wheels but WITHOUT upload ([see details](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-azure))
+- [ ] Create, test and upload manual artifacts
+  - [ ] MacOS package installer (manual task, ask Michael)
+  - [ ] arm64 wheels (manual task, check with Alex or Pramod)
+  - [ ] aarch64 wheels (use existing `release/x.y-aarch64` branch for this, see [guide](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-circleci))
+- [ ] Publish the `x.y.z` wheels on PyPI; see [wheel publishing instructions](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-azure)
+- [ ] Once wheels are published, activate the `x.y.z` tag on ReadTheDocs
+- [ ] Rename the Windows installer in the GitHub release to match the new version and the supported python versions (i.e. `nrn-8.2.2.w64-mingw-py-37-38-39-310-311-setup.exe`)
+- [ ] Publish release on GitHub (edit https://github.com/neuronsimulator/nrn/releases/tag/x.y.z and un-tick the pre-release checkbox)
+
+
+Post-release
+---
+- [ ] Deactivate ReadTheDocs build for `release/x.y`
+- [ ] Go to [ReadTheDocs advanced settings](https://readthedocs.org/dashboard/nrn/advanced/) and set `Default version` to `x.y.z`
+- [ ] Let people know :rocket:
+- [ ] Cherrypick changelog and installer links to `master`
+- [ ] Update the changelog for the release on GitHub
+
+
+Changelog
+======
+
+# NEURON X.Y
+
+## [x.y.z]
+_Release Date_ : DD-MM-YYYY
+
+
+### What's New
+* [List new features/support added]
+* .....
+
+
+### Bug Fixes
+* [List the important bug fixes]
+* ...
+
+
+### Improvements /  Other Changes
+* [List the improvements made in the new release and any other changes]
+* ...
+
+
+For the complete list of commits check  [GitHub Issue #[GH_no.]](https://github.com/neuronsimulator/nrn/issues/#[GH_no.])
+
+ReadTheDocs sneak peek
+======================
+* https://nrn.readthedocs.io/en/release-x.y
+
+Commits going into x.y.z
+========================
+
+[given `a.b.c` is the last release:]
+
+Since [a.b.c], with:
+```bash
+git log --pretty=format:"%h : %s" a.b.c..release/x.y
+```
+we get:
+
+- [ ] commit 1
+- [ ] commit 2
+- [ ] ...

.github/ISSUE_TEMPLATE/release.md

@@ -0,0 +1,110 @@
+---
+name: NEURON Major/Minor Release
+about: Create a NEURON release for a new branch from master.
+title: 'NEURON [x.y.z] release'
+labels: 'release'
+assignees: ''
+
+---
+
+Action items
+============
+
+Pre-release
+---
+- [ ] Make sur to look out for ModelDB regressions by launching analyzing [nrn-modeldb-ci last version vs nightly reports](https://github.com/neuronsimulator/nrn-modeldb-ci/actions/workflows/nrn-modeldb-ci.yaml?query=event%3Aschedule++)
+
+Sanity checks
+---
+- [ ] Create `release/x.y` branch and make sure GitHub, Azure and CircleCI builds pass
+- [ ] Run [nrn-build-ci](https://github.com/neuronsimulator/nrn-build-ci/actions/workflows/build-neuron.yml) for the respective Azure build; see [Azure drop guide](https://github.com/neuronsimulator/nrn-build-ci#azure-wheels-testing---manual-workflow)
+- [ ] Activate ReadTheDocs build for `release/x.y` & make it hidden. Check docs are fine after build is done.
+- [ ] Run BBP Simulation Stack & other relevant tests
+
+
+Releasing
+---
+- [ ] Update semantic version in `CMakeLists.txt`
+- [ ] Update changelog below and agree on it with everyone; then commit it to `docs/changelog` (copy structure as-is)
+- [ ] Update `docs/index.rst` accordingly with the new `.pkg` and `.exe` links for `PKG installer` and `Windows Installer`
+- [ ] Run the ReadTheDocs build again for `release-x.y`, make sure the build passes and inspect the Changelog page.
+- [ ] Create new release+tag on GitHub via [release workflow](https://github.com/neuronsimulator/nrn/actions/workflows/release.yml?query=workflow%3A%22NEURON+Release%22). Note that the GitHub release will be marked as pre-release and  will contain the full-src-package and the Windows installer at the end of the release workflow.
+- [ ] Build release wheels but WITHOUT upload ([see details](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-azure))
+- [ ] Create, test and upload manual artifacts
+  - [ ] MacOS package installer (manual task, ask Michael)
+  - [ ] arm64 wheels (manual task, check with Alex or Pramod)
+  - [ ] aarch64 wheels (create a `release/x.y-aarch64` branch for this, see [guide](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-circleci))
+- [ ] Publish the `x.y.z` wheels on Pypi; see [wheel publishing instructions](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-azure)
+- [ ] Once wheels are published, activate the `x.y.z` tag on ReadTheDocs
+- [ ] Rename the Windows installer in the GitHub release to match the new version and the supported python versions (i.e. `nrn-8.2.2.w64-mingw-py-37-38-39-310-311-setup.exe`
+)
+- [ ] Publish release on GitHub (edit https://github.com/neuronsimulator/nrn/releases/tag/x.y.z and un-tick the pre-release checkbox)
+
+
+Post-release
+---
+- [ ] To mark the start of a new development cycle, tag `master` as follows:
+  - minor version: `x.(y+1).dev`
+  - major version: `(x+1).0.dev`
+- [ ] Deactivate ReadTheDocs build for `release/x.y`
+- [ ] Go to [ReadTheDocs advanced settings](https://readthedocs.org/dashboard/nrn/advanced/) and set `Default version` to `x.y.z`
+- [ ] Let people know :rocket:
+- [ ] Cherrypick changelog and installer links to `master`
+- [ ] Update the changelog for the release on GitHub
+
+Changelog
+======
+
+# NEURON X.Y
+
+## [x.y.z]
+_Release Date_ : DD-MM-YYYY
+
+
+### What's New
+* [List new features/support added]
+* .....
+
+### Breaking Changes
+* [List the changes that aren't backward compatible]
+* ...
+
+
+### Deprecations
+* [List the features that are deprecated]
+* ...
+
+
+### Bug Fixes
+* [List the important bug fixes]
+* ...
+
+
+### Improvements /  Other Changes
+* [List the improvements made in the new release and any other changes]
+* ...
+
+### Upgrade Steps
+* [Describe how to migrate from previous NEURON Version]
+* ...
+
+For the complete list of features and bug fixes, see the list in [GitHub Issue #[GH_no.]](https://github.com/neuronsimulator/nrn/issues/#[GH_no.])
+
+ReadTheDocs sneak peek
+======================
+* https://nrn.readthedocs.io/en/release-x.y
+
+Commits going into x.y.z
+========================
+
+[given `a.b.c` is the last release:]
+
+Since [a.b.c], with:
+```bash
+git log --pretty=format:"%h : %s" a.b.c..release/x.y
+```
+we get:
+
+- [ ] commit 1
+- [ ] commit 2
+- [ ] ...