NEURON 8.2.6 patch release

[heerener]

Action items

Pre-release

• [x] 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
• [ ] Activate ReadtheDocs for the cherry-pick branch and ensure the documentation builds (when logged in, go to the versions page and set the version for your branch to Active and Hidden)
• [ ] Run a test wheel build WITHOUT upload on the cherry-pick branch to ensure all the wheels build (see details)

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
• [ ] 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. 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 Erik, Goran 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 :rocket:
• [ ] Cherrypick changelog and installer links to master
• [ ] Update the changelog for the release on GitHub

Changelog

NEURON 8.2

8.2.6

Release Date : 21-06-2024

What's New

• Pin numpy<2

Bug Fixes

N/A

Improvements / Other Changes

• Pin numpy<2

For the complete list of commits check GitHub Issue #2930

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:

git log --pretty=format:"%h : %s" a.b.c..release/x.y

we get:

• [ ] commit 1
• [ ] commit 2
• [ ] ...

[ramcdougal]

I'm not sure how to add to the cherrypicks, but this is an old bugfix for supporting recent matplotlib that never made it into 8.2.x: https://github.com/neuronsimulator/nrn/commit/8dbd134f2d615835a44702783e6843196d2e70a9

[heerener]

I've added it to the 8.2.6.dev branch Draft PR for now because there may be other changes incoming: https://github.com/neuronsimulator/nrn/pull/2934

[ramcdougal]

For the PKG installer: this should be tested with Anaconda Python on an arm-based mac. from neuron import h failed at the course for someone with this setup who installed using the package but worked when they reinstalled via pip.

Also: why 8.2.6 instead of 8.2.5?

[ramcdougal]

While I'm dreaming, do we have something that solves the backspace problem with nrniv for pip installed versions on a mac? I know @nrnhines looked at this once... the backspace deletes the character from the buffer but not the screen.

[nrnhines]

I see three mentions of this in old PRs and the #2490 (hines/build 8.2.3) and #2486 (hines/fix 8.2.2) mentions refer back to Fixes linux wheel backspace by upgrading ncurses-6.2 to 6.4 #2484.

Presently, I observe (Apple M1. Sonoma 14.5) that the backspace is working.

% unset PYTHONPATH
% python3 -m venv env
% source env/bin/activate
% pip install neuron
Collecting neuron
  Using cached NEURON-8.2.4-cp312-cp312-macosx_12_0_arm64.whl.metadata (3.7 kB)
...
Successfully installed find-libpython-0.4.0 neuron-8.2.4 numpy-2.0.0 packaging-24.1 setuptools-70.1.0
 % env/bin/nrniv
/Users/hines/tmp/env/bin/nrniv:10: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  from pkg_resources import working_set
NEURON -- VERSION 8.2.4 release/8.2 (1d87d5d39) 2024-02-09
Duke, Yale, and the BlueBrain Project -- Copyright 1984-2022
See http://neuron.yale.edu/neuron/credits

<stdin>:149: SyntaxWarning: invalid escape sequence '\.'
<stdin>:197: SyntaxWarning: invalid escape sequence '\.'
oc>

the "invalid escape sequence" messages will be (should be?) gone in the next release because of

commit 4ad8f84d257295339fac1b4eb3028894b3f2c4cb
Author: Michael Hines <michael.hines@yale.edu>
Date:   Tue Feb 20 14:38:27 2024 -0500

    More fixes

    - raw python string needed if escaped dot \. is present avoids syntax warning
    - mistake in conflict resolution of #2733 cherry pick
    - Turn off coreneuron portion of test (or else fix coreneuron)