Merge branch 'neuronsimulator:master' into master

.circleci/config.yml

@@ -1,7 +1,7 @@
 version: 2.1
 
 orbs:
-  python: circleci/python@0.3.2
+  python: circleci/python@2.1.1
 
 jobs:
   manylinux2014-aarch64:
@@ -13,7 +13,7 @@ jobs:
         type: string
 
     machine:
-      image: ubuntu-2004:202101-01
+      image: default
 
     resource_class: arm.medium
 
@@ -49,25 +49,17 @@ jobs:
             # choose available python versions from pyenv
             pyenv_py_ver=""
             case << parameters.NRN_PYTHON_VERSION >> in
-              38) pyenv_py_ver="3.8.7" ;;
-              39) pyenv_py_ver="3.9.1" ;;
-              310) pyenv_py_ver="3.10.1" ;;
-              311) pyenv_py_ver="3.11.0" ;;
-              *) echo "Error: pyenv python version not specified!" && exit 1;;
+              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 or not supported." && exit 1;;
             esac
 
-            # install python dependencies: .10 is not available pyenv
-            if [ "<< parameters.NRN_PYTHON_VERSION >>" == "310" ]; then
-              sudo apt install software-properties-common -y
-              sudo add-apt-repository ppa:deadsnakes/ppa -y
-              sudo apt install python3.10 libpython3.10 python3.10-venv
-              export PYTHON_EXE=$(which python3.10)
-            else
-              cd /opt/circleci/.pyenv/plugins/python-build/../.. && git pull && cd -
-              env PYTHON_CONFIGURE_OPTS="--enable-shared" pyenv install $pyenv_py_ver --force
-              pyenv global $pyenv_py_ver
-              export PYTHON_EXE=$(which python)
-            fi
+            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)
@@ -76,6 +68,7 @@ jobs:
           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
@@ -94,7 +87,7 @@ workflows:
                 - /circleci\/.*/
           matrix:
             parameters:
-              NRN_PYTHON_VERSION: ["311"]
+              NRN_PYTHON_VERSION: ["312"]
               NRN_NIGHTLY_UPLOAD: ["false"]
 
   nightly:
@@ -109,5 +102,5 @@ workflows:
       - manylinux2014-aarch64:
           matrix:
             parameters:
-              NRN_PYTHON_VERSION: ["38", "39", "310", "311"]
+              NRN_PYTHON_VERSION: ["38", "39", "310", "311", "312"]
               NRN_NIGHTLY_UPLOAD: ["true"]

.clang-format.changes

@@ -1,9 +1,10 @@
 SortIncludes: false
 Standard: c++17
-StatementMacros: [MKDLL, MKDLLdec, MKDLLif, MKDLLvp, MKDLLvpf, PyObject_HEAD,
+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,

.github/ISSUE_TEMPLATE/release-patch.md

@@ -13,8 +13,7 @@ Action items
 Pre-release
 ---
 - [ ] Create a cherrypicks branch where all commits go into new release and open a PR against `release/x.y` branch
-- [ ] Create CoreNEURON tag on the `release/x.y` branch after cherrypicking required commits, update semantic version in its `CMakeLists.txt`, tag it & update submodule in cherrypicks PR
-- [ ] 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
+- [ ] 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)
@@ -23,31 +22,32 @@ Pre-release
 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) 
+- [ ] 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, CoreNEURON CI & other relevant tests
-- [ ] 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))
+- [ ] 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.
-- [ ] Create, test and upload manual artifacts 
+- [ ] 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
-- [ ] Upload Windows installer from the wheels publishing Azure run (to get correct tag)
-- [ ] Publish release on GitHub (edit https://github.com/neuronsimulator/nrn/releases/tag/x.y.z and un-tick the pre-release checkbox) 
+- [ ] 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` 
+- [ ] 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

.github/ISSUE_TEMPLATE/release.md

@@ -12,16 +12,14 @@ Action items
 
 Pre-release
 ---
-- [ ] Look out for ModelDB regressions by 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++)
-- [ ] Create CoreNEURON release branch, update semantic version in `CMakeLists.txt`, tag it & update submodule in NEURON
+- [ ] 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) 
+- [ ] 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, CoreNEURON CI & other relevant tests
-- [ ] 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))
+- [ ] Run BBP Simulation Stack & other relevant tests
 
 
 Releasing
@@ -30,26 +28,29 @@ Releasing
 - [ ] 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.
-- [ ] Create, test and upload manual artifacts 
+- [ ] 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
-- [ ] Upload Windows installer from the wheels publishing Azure run (to get correct tag)
+- [ ] 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` 
+  - 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` 
+- [ ] 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
 ======

.github/problem-matchers/thread.json

@@ -0,0 +1,15 @@
+
+{
+  "problemMatcher": [
+      {
+          "owner": "tsan-problem-matcher",
+          "severity": "warning",
+          "pattern": [
+              {
+                  "regexp": "^.*ThreadSanitizer: (.*)$",
+                  "message": 1
+              }
+          ]
+      }
+  ]
+}