Merge branch 'master' into 1uc/fix-nrn_thread_free

.github/ISSUE_TEMPLATE/release-patch.md

@@ -22,31 +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 & 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))
 
 
 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.
-- [ ] Create, test and upload manual artifacts 
+- [ ] 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) 
+- [ ] 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

@@ -17,10 +17,9 @@ Pre-release
 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 & 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))
 
 
 Releasing
@@ -30,6 +29,7 @@ Releasing
 - [ ] 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)
@@ -44,12 +44,13 @@ Releasing
 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
 ======

build_osx_wheels.sh

@@ -0,0 +1,46 @@
+#!/usr/bin/env bash
+
+# This script assumes that you have the prerequisites already installed
+# See https://nrn.readthedocs.io/en/latest/install/python_wheels.html#installing-macos-prerequisites
+#
+# If you want the script to check the nrniv output (for version string checking), set the following environment variable
+# Note that this will require manual intervention during script execution
+#
+# export INTERACTIVE_OK=yes
+
+set -x
+
+export BREW_PREFIX=$(brew --prefix)
+export PATH=/opt/homebrew/opt/bison/bin:/opt/homebrew/opt/flex/bin:$PATH
+
+export NRN_RELEASE_UPLOAD=false
+export NRN_NIGHTLY_UPLOAD=false
+export NEURON_NIGHTLY_TAG=""
+
+export SKIP_EMBEDED_PYTHON_TEST=true
+
+if [ -n $1 ]
+then
+    # example: 9.0a
+    export SETUPTOOLS_SCM_PRETEND_VERSION=$1
+fi
+
+set -e
+
+packaging/python/build_wheels.bash osx 3.9 coreneuron &>3.9-output
+packaging/python/build_wheels.bash osx 3.10 coreneuron &>3.10-output
+packaging/python/build_wheels.bash osx 3.11 coreneuron &>3.11-output
+
+if [ -n $INTERACTIVE_OK ]
+then
+    for py in 9 10 11
+    do
+        python3.${py} -m venv venv3.${py}
+        venv3.${py}/bin/pip install wheelhouse/NEURON-${1}-cp3${py}-cp3${py}-macosx_11_0_arm64.whl
+        venv3.${py}/bin/nrniv
+    done
+fi
+
+bash packaging/python/test_wheels.sh python3.9 wheelhouse/NEURON-*-cp39*.whl true &>3.9-test-output
+bash packaging/python/test_wheels.sh python3.10 wheelhouse/NEURON-*-cp310*.whl true &>3.10-test-output
+bash packaging/python/test_wheels.sh python3.11 wheelhouse/NEURON-*-cp311*.whl true &>3.11-test-output

ci/win_install_deps.cmd

@@ -48,6 +48,14 @@ if "%MSYS2_ROOT%"=="" set MSYS2_ROOT=C:\msys64
 if not exist "%MSYS2_ROOT%\usr\bin\bash.exe" (
     choco install -y --no-progress msys2 --params="/InstallDir:%MSYS2_ROOT% /NoUpdate /NoPath" || goto :error
 )
+
+:: With upgrade of Azure CI runner image on 21st of Sept 2023,
+:: choco brings mingw 12.2.0 and it's somehow incompatible with
+:: msys+neuron installation. So for now, just use previously working
+:: version of mingw
+choco uninstall -y mingw
+choco install --allow-downgrade -y mingw --version=11.2.0
+
 set PATH=%MSYS2_ROOT%\usr\bin;%SystemRoot%\system32;%SystemRoot%;%SystemRoot%\System32\Wbem;%PATH%
 
 :: update pacman cache (sometimes required when new GH/Azure runner images are deployed)

cmake_nrnconf.h.in

@@ -359,7 +359,7 @@
 #include <string_view>
 namespace neuron::config {
 #ifdef USE_PYTHON
-   constexpr std::string_view default_python_executable{"@NRN_DEFAULT_PYTHON_EXECUTABLE@"};
+   constexpr std::string_view default_python_executable{R"(@NRN_DEFAULT_PYTHON_EXECUTABLE@)"};
    constexpr std::array<std::string_view, @NRN_PYTHON_COUNT@> supported_python_versions{@NRN_DYNAMIC_PYTHON_LIST_OF_VERSION_STRINGS@};
 #endif
    constexpr std::string_view shared_library_prefix{"@CMAKE_SHARED_LIBRARY_PREFIX@"};

src/ivoc/xmenu.cpp

@@ -1986,15 +1986,16 @@ void HocValEditor::evalField() {
 }
 
 void HocValEditor::audit() {
-    char buf[200];
+    auto sout = std::stringstream{};
     if (pyvar_) {
         return;
     } else if (variable_) {
-        Sprintf(buf, "%s = %s\n", variable_->string(), fe_->text()->string());
+        sout << variable_->string() << " = " << fe_->text()->string();
     } else if (pval_) {
-        Sprintf(buf, "// %p pointer set to %s\n", pval_, fe_->text()->string());
+        sout << "// " << pval_ << " set to " << fe_->text()->string();
     }
-    hoc_audit_command(buf);
+    auto buf = sout.str();
+    hoc_audit_command(buf.c_str());
 }
 
 void HocValEditor::updateField() {
@@ -2706,13 +2707,16 @@ void OcSlider::update(Observable*) {
 }
 
 void OcSlider::audit() {
+    auto sout = std::stringstream{};
     char buf[200];
+    Sprintf(buf, "%g", *pval_);
     if (variable_) {
-        Sprintf(buf, "%s = %g\n", variable_->string(), *pval_);
+        sout << variable_->string() << " = " << buf << "\n";
     } else if (pval_) {
-        Sprintf(buf, "// %p pointer set to %g\n", pval_, *pval_);
+        sout << "// " << pval_ << " set to " << buf << "\n";
     }
-    hoc_audit_command(buf);
+    auto str = sout.str();
+    hoc_audit_command(str.c_str());
     if (send_) {
         send_->audit();
     }