Merge branch 'fix/kschan-dparam-oob-3843' into pool-cleanup

Author: mgeplf

.github/workflows/neuron-ci.yml

@@ -217,16 +217,17 @@ jobs:
         # A automake >= 1.16.5 is needed for python 3.12 because it generates a python script
         # called py-compile and the original one is not supporting this version of python
         # Once ubuntu got a newer version of automake we can remove this part.
+        # Tarball from ci-deps-v1 via ci/deps (see MANIFEST id automake-1.16.5-src).
         if: matrix.config.music == 'ON' && startsWith(matrix.os, 'ubuntu')
         run: |
-          curl -L -o automake.tar.xz https://ftpmirror.gnu.org/gnu/automake/automake-1.16.5.tar.xz
-          tar -xf automake.tar.xz
-          cd automake-1.16.5/
+          export NRN_CI_DEPS_SOURCE=release
+          bash "${{ github.workspace }}/ci/deps/fetch.sh" automake-1.16.5-src "${{ runner.temp }}"
+          tar -xf "${{ runner.temp }}/automake-1.16.5.tar.xz" -C "${{ runner.temp }}"
+          cd "${{ runner.temp }}/automake-1.16.5/"
           ./configure --prefix=/usr/
           make -j
           sudo make -j install
           automake --version
-        working-directory: ${{runner.temp}}
 
       - name: Setup MUSIC@${{ env.MUSIC_VERSION }}
         if: matrix.config.music == 'ON'

.github/workflows/release.yml

@@ -85,7 +85,9 @@ jobs:
     needs:
       - build-wheels
     outputs:
-      artifacts-url: ${{ steps.merge-artifacts.outputs.artifacts-url }}
+      # upload-artifact/merge@v4 exports artifact-url (singular), not artifacts-url.
+      # Job output key stays artifacts-url for existing consumers (modeldb-ci, build-ci).
+      artifacts-url: ${{ steps.merge-artifacts.outputs.artifact-url }}
     steps:
       - name: Merge Artifacts
         id: merge-artifacts

.github/workflows/wheels-template.yml

@@ -114,12 +114,12 @@ jobs:
           sudo bash packaging/python/build_static_readline_osx.bash
 
       - name: Change name of package for release
-        if: inputs.build_type == 'release'
+        if: inputs.build_type == 'nightly'
         run: |
           python3 -m venv venv
           source venv/bin/activate
           python3 -m pip install tomli tomli-w
-          python3 packaging/python/change_name.py ./pyproject.toml neuron
+          python3 packaging/python/change_name.py ./pyproject.toml neuron-nightly
 
       - name: Optimize RX3D Python module
         if: inputs.optimize_rxd == true
@@ -151,18 +151,9 @@ jobs:
         run: |
           sudo apt update
           sudo apt install -y mpich openmpi-bin libopenmpi-dev libmpich-dev ninja-build
-
-      - name: "Apply workaround for MPICH on Ubuntu 24.04"
-        if: inputs.platform == 'ubuntu-24.04'
-        run: |
-          # mpich is fundamentally broken on Ubuntu 24.04 LTS, for more details see:
-          # https://bugs.launchpad.net/ubuntu/+source/mpich/+bug/2072338
-          # This is fixed in version 4.2.0-5.1, but this version has not been
-          # backported, so as a workaround, we install that version manually
-          sudo apt install -y mpich
-          wget 'https://launchpad.net/ubuntu/+source/mpich/4.2.0-5.1/+build/28285882/+files/mpich_4.2.0-5.1_amd64.deb'
-          wget 'https://launchpad.net/ubuntu/+source/mpich/4.2.0-5.1/+build/28285882/+files/libmpich12_4.2.0-5.1_amd64.deb'
-          sudo dpkg --install mpich_4.2.0-5.1_amd64.deb libmpich12_4.2.0-5.1_amd64.deb
+          # Ubuntu 24.04: pin working mpich from ci/deps (no Launchpad download).
+          # See ci/deps/README.md and LP#2072338.
+          bash ci/deps/install_mpich_noble.sh
 
       - name: Set env vars for testing (Linux)
         if: startsWith(inputs.platform, 'ubuntu')

.gitignore

@@ -22,6 +22,8 @@ virtualenv
 *.lo
 docs/_build
 docs/_generated
+# CI managed-download scratch (publish.sh); blobs live on GitHub Releases
+ci/deps/assets/
 .vscode
 .coverage*
 coverage*.xml

CMakeLists.txt

@@ -216,7 +216,7 @@ set(NRN_RX3D_OPT_LEVEL
     "${NRN_RX3D_OPT_LEVEL_DEFAULT}"
     CACHE STRING "Optimization level for Cython generated files (non-zero may compile slowly)")
 
-option(NRN_ENABLE_COVERAGE "EnableCode Coverage (make cover_begin, make cover_html)" OFF)
+option(NRN_ENABLE_COVERAGE "EnableCode Coverage (cover-begin, cover-html, cover-diff)" OFF)
 set(NRN_COVERAGE_FILES
     ""
     CACHE STRING "semicolon (;) separated list of files to collect code coverage")

azure-pipelines.yml

@@ -81,21 +81,9 @@ stages:
       - script: |
           sudo apt update
           sudo apt install -y mpich openmpi-bin libopenmpi-dev libmpich-dev
-          # mpich is fundamentally broken on Ubuntu 24.04 LTS, for more details see:
-          # https://bugs.launchpad.net/ubuntu/+source/mpich/+bug/2072338
-          # This is fixed in version 4.2.0-5.1, but this version has not been
-          # backported, so as a workaround, we install that version manually
-          source /etc/os-release
-          if [[ "$ID" == "ubuntu" && "$VERSION_ID" == "24.04" ]]; then
-            # mpich is fundamentally broken on Ubuntu 24.04 LTS, for more details see:
-            # https://bugs.launchpad.net/ubuntu/+source/mpich/+bug/2072338
-            # This is fixed in version 4.2.0-5.1, but this version has not been
-            # backported, so as a workaround, we install that version manually
-            sudo apt install -y mpich
-            wget 'https://launchpad.net/ubuntu/+source/mpich/4.2.0-5.1/+build/28285882/+files/mpich_4.2.0-5.1_amd64.deb'
-            wget 'https://launchpad.net/ubuntu/+source/mpich/4.2.0-5.1/+build/28285882/+files/libmpich12_4.2.0-5.1_amd64.deb'
-            sudo dpkg --install mpich_4.2.0-5.1_amd64.deb libmpich12_4.2.0-5.1_amd64.deb
-          fi
+          # Ubuntu 24.04: pin working mpich from ci/deps (no Launchpad download).
+          # See ci/deps/README.md and LP#2072338.
+          ci/deps/install_mpich_noble.sh
         displayName: 'Install Test System Dependencies'
 
       - template: ci/azure-wheel-test-upload.yml

bin/CMakeLists.txt

@@ -38,6 +38,8 @@ include(CMakeListsNrnMech)
 # =============================================================================
 configure_file("nrngui.in" "nrngui" @ONLY)
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/sortspike ${CMAKE_CURRENT_BINARY_DIR}/sortspike COPYONLY)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/rdcellstate ${CMAKE_CURRENT_BINARY_DIR}/rdcellstate
+               COPYONLY)
 configure_file(${CMAKE_CURRENT_SOURCE_DIR}/nrnivmodl_makefile_cmake.in
                ${PROJECT_BINARY_DIR}/bin/nrnmech_makefile @ONLY)
 string(JOIN " " NRN_PYTHON_VERSIONS_STRING ${NRN_PYTHON_VERSIONS})
@@ -98,6 +100,7 @@ if(NRN_ENABLE_CORENEURON)
 endif()
 
 install(FILES ${PROJECT_BINARY_DIR}/bin/nrnmech_makefile DESTINATION ${NRN_INSTALL_DATA_PREFIX}bin)
-install(PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/sortspike ${CMAKE_CURRENT_SOURCE_DIR}/mkthreadsafe
-                 ${PROJECT_BINARY_DIR}/bin/nrnpyenv.sh ${CMAKE_CURRENT_SOURCE_DIR}/set_nrnpyenv.sh
-        DESTINATION ${NRN_INSTALL_DATA_PREFIX}bin)
+install(
+  PROGRAMS ${CMAKE_CURRENT_BINARY_DIR}/sortspike ${CMAKE_CURRENT_BINARY_DIR}/rdcellstate
+           ${CMAKE_CURRENT_SOURCE_DIR}/mkthreadsafe ${PROJECT_BINARY_DIR}/bin/nrnpyenv.sh
+           ${CMAKE_CURRENT_SOURCE_DIR}/set_nrnpyenv.sh DESTINATION ${NRN_INSTALL_DATA_PREFIX}bin)

bin/rdcellstate

@@ -0,0 +1,5 @@
+#!/usr/bin/env python3
+"""Thin CLI wrapper for neuron.debug.rdcellstate."""
+from neuron.debug.rdcellstate import main
+
+raise SystemExit(main())

ci/coverage_files_from_diff.sh

@@ -0,0 +1,14 @@
+#!/usr/bin/env bash
+# Emit a semicolon-separated source file list for -DNRN_COVERAGE_FILES=...
+# Usage: coverage_files_from_diff.sh [base-ref]
+# Default base-ref is master (three-dot diff: base...HEAD).
+# Exits 1 with a stderr message when no compiled sources (.cpp/.c) changed.
+set -euo pipefail
+
+base="${1:-master}"
+mapfile -t files < <(git diff --name-only "${base}...HEAD" | grep -E '\.(cpp|c)$' || true)
+if ((${#files[@]} == 0)); then
+  echo "No compiled sources (.cpp/.c) changed vs ${base}; omit -DNRN_COVERAGE_FILES" >&2
+  exit 1
+fi
+(IFS=';'; echo "${files[*]}")

ci/deps/MANIFEST.yml

@@ -0,0 +1,198 @@
+# NEURON CI dependency archive (catalog)
+#
+# Purpose: pin external CI downloads on a GitHub Release, prefer those over flaky
+# third-party hosts, and make upgrades explicit (update this file; re-publish;
+# run check-upstream.sh). Binary blobs are NOT committed under ci/deps/assets/
+# (that directory is gitignored scratch for publish.sh).
+#
+# Fetch order used by fetch.sh (unless NRN_CI_DEPS_SOURCE is set):
+#   1. local   — ci/deps/assets/<file>  (optional local scratch; not in git)
+#   2. release — ${NRN_CI_DEPS_BASE_URL}/<file> or default_release_base_url
+#   3. upstream — upstream_url (last resort)
+#
+# managed:
+#   true  — pin hosted on our GitHub Release (ci-deps-vN); CI should use fetch.sh
+#   false — catalog row only; not yet switched off upstream
+#
+# See ci/deps/README.md
+
+version: 1
+
+# GitHub Release assets for managed pins (override with NRN_CI_DEPS_BASE_URL).
+# Host repo is neuronsimulator/nrn-ci-deps (not product releases on nrn).
+# Navigate: https://github.com/neuronsimulator/nrn-ci-deps/releases → tag ci-deps-v1
+default_release_base_url: "https://github.com/neuronsimulator/nrn-ci-deps/releases/download/ci-deps-v1"
+
+assets:
+  # --- P0: wheel-test MPICH workaround (Ubuntu 24.04 / noble) ---
+  - id: mpich-noble-4.2.0-5.1
+    file: mpich_4.2.0-5.1_amd64.deb
+    sha256: c696dff0975f1857faaae0e450ce6262d13693a7894e523741e6b7581beee0ad
+    upstream_url: https://launchpad.net/ubuntu/+source/mpich/4.2.0-5.1/+build/28285882/+files/mpich_4.2.0-5.1_amd64.deb
+    managed: true
+    consumers:
+      - azure-pipelines.yml
+      - .github/workflows/wheels-template.yml
+      - ci/deps/install_mpich_noble.sh
+    notes: >
+      Ubuntu 24.04 LP#2072338 workaround. Pair with libmpich12-noble-4.2.0-5.1.
+      Only needed while distro mpich remains broken for our tests.
+
+  - id: libmpich12-noble-4.2.0-5.1
+    file: libmpich12_4.2.0-5.1_amd64.deb
+    sha256: 13a233b7dd6d8a51eccf58d981cdb1ae110b673e4dfdeb607fe439918340238f
+    upstream_url: https://launchpad.net/ubuntu/+source/mpich/4.2.0-5.1/+build/28285882/+files/libmpich12_4.2.0-5.1_amd64.deb
+    managed: true
+    consumers:
+      - azure-pipelines.yml
+      - .github/workflows/wheels-template.yml
+      - ci/deps/install_mpich_noble.sh
+    notes: Runtime library package for mpich-noble-4.2.0-5.1.
+
+  - id: mpich-noble-4.2.0-5.1-arm64
+    file: mpich_4.2.0-5.1_arm64.deb
+    sha256: c790342026ca5786bdad889af5b2c6f4c249bb07968aaf5435feb6b2771df452
+    upstream_url: https://launchpad.net/ubuntu/+source/mpich/4.2.0-5.1/+build/28285883/+files/mpich_4.2.0-5.1_arm64.deb
+    managed: true
+    consumers:
+      - .github/workflows/wheels-template.yml
+      - ci/deps/install_mpich_noble.sh
+    notes: >
+      arm64 counterpart of mpich-noble-4.2.0-5.1 (Launchpad build 28285883).
+      Pair with libmpich12-noble-4.2.0-5.1-arm64. Used by ubuntu-24.04-arm wheel tests.
+
+  - id: libmpich12-noble-4.2.0-5.1-arm64
+    file: libmpich12_4.2.0-5.1_arm64.deb
+    sha256: 4fdbdcdcf23a36f3f7fcd2f2fe2fdaff24629a107fa9f0c6904dd1c3aa662ae1
+    upstream_url: https://launchpad.net/ubuntu/+source/mpich/4.2.0-5.1/+build/28285883/+files/libmpich12_4.2.0-5.1_arm64.deb
+    managed: true
+    consumers:
+      - .github/workflows/wheels-template.yml
+      - ci/deps/install_mpich_noble.sh
+    notes: Runtime library package for mpich-noble-4.2.0-5.1-arm64.
+
+  # --- P0/P1: static readline/ncurses sources (GNU mirrors flake) ---
+  - id: ncurses-6.4-src
+    file: ncurses-6.4.tar.gz
+    sha256: 6931283d9ac87c5073f30b6290c4c75f21632bb4fc3603ac8100812bed248159
+    upstream_url: https://ftp.gnu.org/gnu/ncurses/ncurses-6.4.tar.gz
+    managed: true
+    consumers:
+      - packaging/python/build_static_readline_osx.bash
+      - packaging/python/Dockerfile
+    notes: Hosted on ci-deps-v1; consumers must not use ftpmirror.gnu.org.
+
+  - id: readline-7.0-src
+    file: readline-7.0.tar.gz
+    sha256: 750d437185286f40a369e1e4f4764eda932b9459b5ec9a731628393dd3d32334
+    upstream_url: https://ftp.gnu.org/gnu/readline/readline-7.0.tar.gz
+    managed: true
+    consumers:
+      - packaging/python/Dockerfile
+    notes: >
+      Linux manylinux Dockerfile uses 7.0. Azure Mac wheels use prebuilt secure
+      file readline7.0-ncurses6.4.tar.gz (not in this manifest yet).
+
+  - id: readline-8.3-src
+    file: readline-8.3.tar.gz
+    sha256: fe5383204467828cd495ee8d1d3c037a7eba1389c22bc6a041f627976f9061cc
+    upstream_url: https://ftp.gnu.org/gnu/readline/readline-8.3.tar.gz
+    managed: true
+    consumers:
+      - packaging/python/build_static_readline_osx.bash
+    notes: >
+      GH Actions Mac wheels rebuild from 8.3 every job — version skew vs Azure 7.0
+      prebuilt. Unify in a later PR.
+
+  # --- P1: Windows installer toolchain ---
+  - id: nsis-3.05
+    file: nsis-3.05-setup.exe
+    sha256: ""  # fill when vendoring; SourceForge redirects make automated HEAD unreliable
+    upstream_url: http://prdownloads.sourceforge.net/nsis/nsis-3.05-setup.exe
+    managed: false
+    consumers:
+      - ci/win_download_deps.cmd
+    notes: SourceForge historically flaky.
+
+  - id: envar-plugin-0.3.1
+    file: EnVar-Plugin.zip
+    sha256: e5b337fcad68252d18282f7259a0306053626e41b9480fa09df3fab012b85e00
+    upstream_url: https://github.com/GsNSIS/EnVar/releases/download/v0.3.1/EnVar-Plugin.zip
+    managed: false
+    consumers:
+      - ci/win_download_deps.cmd
+
+  - id: msmpi-runtime
+    file: msmpisetup.exe
+    sha256: ""
+    upstream_url: https://download.microsoft.com/download/a/5/2/a5207ca5-1203-491a-8fb8-906fd68ae623/msmpisetup.exe
+    managed: false
+    consumers:
+      - ci/win_download_deps.cmd
+    notes: Opaque Microsoft CDN path; pin by URL + hash when vendoring.
+
+  - id: msmpi-sdk
+    file: msmpisdk.msi
+    sha256: ""
+    upstream_url: https://download.microsoft.com/download/a/5/2/a5207ca5-1203-491a-8fb8-906fd68ae623/msmpisdk.msi
+    managed: false
+    consumers:
+      - ci/win_download_deps.cmd
+
+  # --- P1/P2: occasional CI tools ---
+  - id: ccache-4.11.3-linux-x86_64
+    file: ccache-4.11.3-linux-x86_64.tar.xz
+    sha256: 7766991b91b3a5a177ab33fa043fe09e72c68586d5a86d20a563a05b74f119c0
+    upstream_url: https://github.com/ccache/ccache/releases/download/v4.11.3/ccache-4.11.3-linux-x86_64.tar.xz
+    managed: false
+    consumers:
+      - .github/workflows/coverage.yml
+    notes: Already on GitHub releases; low flake priority.
+
+  - id: automake-1.16.5-src
+    file: automake-1.16.5.tar.xz
+    sha256: f01d58cd6d9d77fbdca9eb4bbd5ead1988228fdb73d6f7a201f5f8d6b118b469
+    upstream_url: https://ftp.gnu.org/gnu/automake/automake-1.16.5.tar.xz
+    managed: true
+    consumers:
+      - .github/workflows/neuron-ci.yml
+    notes: Ubuntu MUSIC job path (neuron-ci); needs automake >= 1.16.5 for Python 3.12.
+
+  # --- Azure-only secure files (document; not managed by fetch.sh yet) ---
+  - id: azure-secure-readline7.0-ncurses6.4
+    file: readline7.0-ncurses6.4.tar.gz
+    sha256: ""
+    upstream_url: ""
+    managed: false
+    consumers:
+      - azure-pipelines.yml
+    notes: Azure Pipelines secure file (prebuilt Mac static libs). Prefer migrating to this archive.
+
+  - id: azure-secure-mpt-headers-2.21
+    file: mpt_headears.2.21.tar.gz
+    sha256: ""
+    upstream_url: ""
+    managed: false
+    consumers:
+      - azure-pipelines.yml
+    notes: Azure secure file for SGI MPT headers (dynamic MPI in Linux wheels). Typo "headears" is the uploaded name.
+
+  # --- Tier B (large; usually reliable; managed: false for now) ---
+  - id: python-3.10.0-amd64-exe
+    file: python-3.10.0-amd64.exe
+    sha256: ""
+    upstream_url: https://www.python.org/ftp/python/3.10.0/python-3.10.0-amd64.exe
+    managed: false
+    consumers:
+      - ci/win_download_deps.cmd
+    notes: ~28 MB; self-host only if python.org flakes.
+
+  - id: python-3.14.0-macos11-pkg
+    file: python-3.14.0-macos11.pkg
+    sha256: ""
+    upstream_url: https://www.python.org/ftp/python/3.14.0/python-3.14.0-macos11.pkg
+    managed: false
+    consumers:
+      - azure-pipelines.yml
+      - .github/workflows/wheels-template.yml
+    notes: Representative Mac python.org installer; matrix has one pkg per Python version.