NEURON 9.0.2 patch release

[nrnhines]

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)
• 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 and Azure 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)
• Publish the x.y.z wheels on PyPI; see wheel publishing instructions
• Once wheels are published, activate the x.y.z tag on ReadTheDocs
• 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 to master
• Update the changelog for the release on GitHub
• Update codemeta.json (master branch only) with the new version, changelog, date, and links

Changelog

NEURON 9.0.2

9.0.2

Release Date : DD-MM-YYYY

What's New

• Documentation enhancements (typo fixes (1.9 -> 1e9 for large dt #3754, Python typo fix #3776), contributing documentation (How to contribute to Documentation #3721), C API corrections (fix section pushing examples in C API docs #3785))

Bug Fixes

• Import3D on mac can now detect swc files (fix for file type detection on linux and mac #3788)
• rxd fixed-step extracellular Neumann boundary conditions corrected (Fix the Neumann BC in the x-direction of fixed step extracellular diffusion. #3690)
• Vector.min_ind(i1, i2) fix (Fix Vector.min_ind(i1, i2) bug #3787)
• iterating over segments with no mechanisms no longer segfaults (handle segment iteration when no mechs #3794)
• buffer overflow in output_spikes_parallel prevention (Fix buffer overflow in output_spikes_parallel with zero spikes #3813)

Improvements / Other Changes

• C API always returns current diameter (Recompute 3d-derived diam in nrn_segment_diam_get #3814), supports top-level runtime scalars (Add nrn_global_double_get/set for top-level HOC scalars #3815)
• rxd reaction compilation now supports np.float64 and other np.generic types (rxd handles np.float64 #3808)
• NMODL compiler enhancements (Handle state_discontinuity call in NET_RECEIVE block #3592, Add codegen for implicit diam and area #3631, Add explicit METHOD to SOLVE if target is a DERIVATIVE block #3600, Add unrolling of FROM iteration variables #3597, Generalize MergeInitialBlocksVisitor #3598, NMODL: make v, celsius, and dt available in VERBATIM #3740)
• CI is more robust (ci: for macosx wheels, try to use system clang. #3730, Retry 3 times when downloading from gnu mirrors #3809)

For the complete list of commits check GitHub Issue #3816

ReadTheDocs sneak peek

• https://nrn.readthedocs.io/en/902-cherrypick

Commits going into 9.0.2

[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:

• 45eaf25 : neuronapi: fix nrn_symbol_dataptr for top-level runtime scalars (Add nrn_global_double_get/set for top-level HOC scalars #3815)
• 31b61e4 : neuronapi: recompute 3d-derived diam in nrn_segment_diam_get (Recompute 3d-derived diam in nrn_segment_diam_get #3814)
• ea161e7 : Fix buffer overflow in output_spikes_parallel with zero spikes (Fix buffer overflow in output_spikes_parallel with zero spikes #3813)
• 401fa55 : Retry 3 times when downloading from gnu mirrors (Retry 3 times when downloading from gnu mirrors #3809)
• f2e66b8 : Fix install docs: minimum Python version is 3.10 (Fix install docs: minimum Python version is 3.10 #3806)
• fba971b : rxd handles np.float64 and other numpy.generic types (rxd handles np.float64 #3808)
• 288345e : fix for file type detection on linux and mac (fix for file type detection on linux and mac #3788)
• 722facf : Fix Vector.min_ind(i1, i2) bug (Fix Vector.min_ind(i1, i2) bug #3787)
• 34f2ba7 : handle segment iteration when no mechs (handle segment iteration when no mechs #3794)
• dbfe378 : fix section pushing examples in C API docs (fix section pushing examples in C API docs #3785)
• 646b594 : Python typo fix (Python typo fix #3776)
• 202b83f : updated cmake documentation link (updated cmake documentation link #3775)
• 0402046 : CTNG cleanup (CTNG cleanup #3564)
• c1205a0 : removed link to page that doesn't exist in current docs (removed link to page that doesn't exist in current docs #3731)
• 428e923 : 1.9 -> 1e9 for large dt (1.9 -> 1e9 for large dt #3754)
• 859a5c2 : Bump minimal python to 3.10 (Bump minimal python to 3.10 #3745)
• f7c8be7 : more neutral language (more neutral language #3739)
• ed67703 : NMODL: make v, celsius, and dt available in VERBATIM (NMODL: make v, celsius, and dt available in VERBATIM #3740)
• 5829f9e : FAQ comment about GUI. (FAQ comment about GUI. #3738)
• 46d60d8 : fix: make Sprintf interpret %% -> % correctly when no args are passed (fix: make Sprintf interpret %% -> % correctly when no args are passed #3727)
• 6633938 : ci: for macosx wheels, try to use system clang. (ci: for macosx wheels, try to use system clang. #3730)
• adb42dc : link back to forum (link back to forum #3726)
• 91aecd2 : Bump tornado from 6.5.1 to 6.5.5 in /ci (Bump tornado from 6.5.1 to 6.5.5 in /ci #3723)
• 458cb90 : Update forum link to NEURON discussion board (Update forum link to NEURON discussion board #3724)
• 646c9ac : How to contribute to Documentation (How to contribute to Documentation #3721)
• 5856cf8 : link updates to readthedocs (link updates to readthedocs #3718)
• b68a26b : NMODL: Generalize MergeInitialBlocksVisitor (Generalize MergeInitialBlocksVisitor #3598)
• 1c78186 : Add unrolling of FROM iteration variables (Add unrolling of FROM iteration variables #3597)
• 458e1ff : Add explicit METHOD to SOLVE if target is a DERIVATIVE block (Add explicit METHOD to SOLVE if target is a DERIVATIVE block #3600)
• fe89e7a : NMODL: Add codegen for implicit diam and area (Add codegen for implicit diam and area #3631)
• baeee71 : Bump bokeh from 3.7.2 to 3.8.2 in /ci (Bump bokeh from 3.7.2 to 3.8.2 in /ci #3691)
• ac1b258 : Fix the Neumann BC in the x-direction of fixed step extracellular diffusion. (Fix the Neumann BC in the x-direction of fixed step extracellular diffusion. #3690)
• d8a28e8 : NMODL: Handle state_discontinuity call in NET_RECEIVE block (Handle state_discontinuity call in NET_RECEIVE block #3592)
• da8cb96 : Bump urllib3 from 2.6.0 to 2.6.3 in /ci (Bump urllib3 from 2.6.0 to 2.6.3 in /ci #3693)
• 8efb550 : Add NMODL development guide (Add NMODL development guide #3683)
• 17ae82f : Bump urllib3 from 2.5.0 to 2.6.0 in /ci (Bump urllib3 from 2.5.0 to 2.6.0 in /ci #3681)
• 5105ca3 : Fix Python extension library name (Fix Python lib name #3679)

[ramcdougal]

Cherrypicks: #3817

Readthedocs: https://www.neuronsimulator.org/en/902-cherrypick/

[nrnhines]

nrn-modeldb-ci compared NEURON version 9.0.1 with 9.0.1-40-gf548563fe . Both had 1 failed model 2018260, no failed runs, and 48 skipped runs. The total number of models run was 806. No models had gout files that differed. I conclude that nrn-modeldb-ci passes.

As an aid to to me in reproducing these results (or rerunning in case the PR changes significantly) here are the commands used and a <few notes>.

git@github.com:neuronsimulator/nrn-modeldb-ci
<branch: hines/runtime    commit 4d7e8ad30    README has instructions on usage>
python3.13 -m venv env313
source env313/bin/activate
pip install -e .
pip install neuron  <9.0.1>
<I already had models from getmodels>
runmodels --workdir=9.0.1
<somewhere build and install NEURON for branch 902-cherrypick. Use python3.13>
< see  Working with a local build of NEURON with regard to exporting NRNHOME, NEURONHOME, PATH, and PYTHONPATH
    perhaps best in another terminal (with source env313/bin/activate)to make it easy to get
    back to 9.0.1 in the first terminaL>
runmodels --workdir=902
diffreports2html 9.0.1.json 902.json
show_diff_gout 9.0.1 902