NEURON 8.2.4 patch release

[heerener]

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 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 for the release/x.y branch; see nrn-build-ci guide # it's broken, but the whole point of this release is to prepare to fix that
• Activate ReadTheDocs build for release/x.y & make it hidden. Check docs are fine after build is done. (see Failure to build docs on release 8.2  #2710. EDIT 2: works now with one particular subsection of an RX3D notebook removed)
• Run BBP Simulation Stack & other relevant tests

Releasing

• Create new release+tag on GitHub via release workflow. 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)
• 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)
• Publish the x.y.z wheels on PyPI; see wheel publishing instructions
• 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 and set Default version to x.y.z
• Let people know 🚀
• Cherrypick changelog and installer links to master
• Update the changelog for the release on GitHub

Changelog

NEURON 8.2

8.2.4

Release Date : 06-02-2024

What's New

Bug Fixes

• Python 3.12 compatibility fixes
  • replace distutils with setuptools
  • fix segfault on exit
• updates to CI
  • move from MacOS 11 to MacOS 12
  • add MUSIC
  • bugfix for coverage CI
• small bugfix for edge case in RX3D
• unified setup.py
• misc cmake improvements

Improvements / Other Changes

• Disabled RXD code in notebook to avoid breaking docs build (see GitHub Issue #2710)
• Disabled RXD tests on Windows (see GitHub Issue #2585)

For the complete list of commits check GitHub Issue #2700

ReadTheDocs sneak peek

• https://nrn.readthedocs.io/en/release-x.y

Commits going into 8.2.4

Since [8.2.3], with:

git log --pretty=format:"%h : %s" 8.2.3..release/8.2

we get:

8e483a9 : pin packaging==21.3 (#2707)
b4c5480 : readthedocs: update config
19037ae : 8.2.4 version bump
1011e38 : Add FastDebug as CMAKE_BUILD_TYPE (#2704)
b80818c : Fix segfault on Python 3.12 (#2695)
ed59fa4 : CI: fix installation of MUSIC
f8b36b2 : CI: move from MacOS 11 to MacOS 12
622c961 : Fix RX3D test (#2676)
a9b1632 : Fix cmake formatting
973c0e8 : Fix missing requirements in coverage CI
2c03d4b : Update ci/win_install_deps.cmd
86cf43a : Add an ENVIRONMENT option to nrn_add_test_group (#1885)
9b6ef30 : Remove unused nmodl tests
9b41948 : Move strtobool to correct dir
636b990 : Pin Cython dependency when installing MUSIC in CI
a207c31 : Fix missing init.py
4214aae : Fix CoreNEURON test
00d29df : setup.py: fix method call
772a624 : setup.py: fix missing package file
eba672c : setup.py: fix missing symbols
e985d6b : setup.py: configure RX3D for hoc_module (#2272)
d7ec2ca : Pin cython to < 3. Workaround for #2430 (#2433)
e3dd7df : Reintroduce Cython<3 for ABI compatibility
f64e5db : Fix version issues
cd26025 : Remove setup.py.in for MUSIC
973fc62 : one setup.py to rule them all (#2235)
75599aa : remove distutils usage + fix & add MUSIC basic CI tests (#2193)

• ...