Merge branch 'master' into fix-doc-warning-format

Author: Shamloor

.github/workflows/formatting.yml

@@ -18,7 +18,7 @@ on:
 jobs:
   all:
     name: C/C++, CMake and Python
-    runs-on: ubuntu-22.04
+    runs-on: ubuntu-24.04
     timeout-minutes: 5
     steps:
       - uses: actions/checkout@v4

.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/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

@@ -19,7 +19,7 @@ project(
   NEURON
   VERSION 9.0.1
   LANGUAGES C CXX
-  HOMEPAGE_URL "https://nrn.readthedocs.io/")
+  HOMEPAGE_URL "https://www.neuronsimulator.org/")
 
 # =============================================================================
 # CMake common project settings
@@ -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")
@@ -949,21 +949,43 @@ add_custom_target(
   COMMAND ${PROJECT_SOURCE_DIR}/external/coding-conventions/bin/format
   WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
 
-# Prepare a shell script to format only files modified with respect to master branch
+# Prepare a shell script to format only files modified with respect to master/main branch that still
+# exist on disk (filters out deleted files).
 file(
   WRITE ${CMAKE_CURRENT_BINARY_DIR}/format-pr.sh
-  "\
-#!bash\n\
-set -e\n\
-cmd='cd ${PROJECT_SOURCE_DIR} && external/coding-conventions/bin/format `git diff --name-only master`'\n\
-echo $cmd\n\
-cd ${PROJECT_SOURCE_DIR} && external/coding-conventions/bin/format `git diff --name-only master`\n\
+  "#!/bin/bash
+set -euo pipefail
+
+# Try 'main' first, then fall back to 'master'
+for base in main master; do
+    if git rev-parse --verify \"\$base\" >/dev/null 2>&1; then
+        BASE_BRANCH=\"\$base\"
+        break
+    fi
+done
+
+if [ -z \"\${BASE_BRANCH:-}\" ]; then
+    echo \"Error: Neither 'main' nor 'master' branch found.\" >&2
+    exit 1
+fi
+
+echo \"Formatting changes vs '\$BASE_BRANCH' (existing files only)...\" >&2
+
+# Get changed files (null-delimited so names with spaces work), only pass
+# files that still exist.
+git diff -z --name-only \"\$BASE_BRANCH\" | \\
+while IFS= read -r -d '' file; do
+    if [ -e \"\$file\" ]; then
+        printf '%s\\0' \"\$file\"
+    fi
+done | \\
+xargs -0 --no-run-if-empty external/coding-conventions/bin/format \"\$@\"
 ")
 
 add_custom_target(
   format-pr
   COMMAND bash ${CMAKE_CURRENT_BINARY_DIR}/format-pr.sh
-  COMMENT "Format only files modified with respect to master branch."
+  COMMENT "Format only files modified with respect to main/master (existing files only)"
   WORKING_DIRECTORY ${PROJECT_SOURCE_DIR})
 
 # =============================================================================

README.md

@@ -1,7 +1,7 @@
 [![Build Status](https://dev.azure.com/neuronsimulator/nrn/_apis/build/status/neuronsimulator.nrn?branchName=master)](https://dev.azure.com/neuronsimulator/nrn/_build/latest?definitionId=1&branchName=master) [![Actions Status](https://github.com/neuronsimulator/nrn/actions/workflows/windows.yml/badge.svg?branch=master)](https://github.com/neuronsimulator/nrn/actions) [![Actions Status](https://github.com/neuronsimulator/nrn/workflows/NEURON%20CI/badge.svg)](https://github.com/neuronsimulator/nrn/actions) [![codecov](https://codecov.io/gh/neuronsimulator/nrn/branch/master/graph/badge.svg?token=T7PIDw6LrC)](https://codecov.io/gh/neuronsimulator/nrn) [![Documentation Status](https://readthedocs.org/projects/nrn/badge/?version=latest)](http://nrn.readthedocs.io/?badge=latest)
 
 # NEURON
-NEURON is a simulator for models of neurons and networks of neuron. See [nrn.readthedocs.io](https://nrn.readthedocs.io) for documentation, tutorials, and announcements of courses and conferences. Installers are available on [GitHub Releases](https://github.com/neuronsimulator/nrn/releases) and the source code on [GitHub](https://github.com/neuronsimulator/nrn).
+NEURON is a simulator for models of neurons and networks of neuron. See [https://www.neuronsimulator.org](https://www.neuronsimulator.org) for documentation, tutorials, and announcements of courses and conferences. Installers are available on [GitHub Releases](https://github.com/neuronsimulator/nrn/releases) and the source code on [GitHub](https://github.com/neuronsimulator/nrn).
 Ask questions on our [Discussion Forum](https://github.com/neuronsimulator/nrn/discussions).
 
 ## Installing NEURON
@@ -26,7 +26,7 @@ It is possible to install the Linux Python wheels on Windows via the Windows Sub
 
 ## Documentation
 
-* See [https://nrn.readthedocs.io/en/latest/](https://nrn.readthedocs.io/en/latest/) for latest, nightly snapshot
+* See [https://www.neuronsimulator.org/en/latest/](https://www.neuronsimulator.org/en/latest/) for latest, nightly snapshot
 * See [docs/README.md](docs/README.md) for information on documentation (local build, Read the Docs setup)
 
 ## Changelog

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/nrnivmodl.in

@@ -287,7 +287,7 @@ make -j 4 -f "${bindir}/nrnmech_makefile" "ROOT=${prefix}" "MODOBJFILES=$MODOBJS
      echo "Successfully created $MODSUBDIR/special"
  else
      printf "\nNOTE: If you are encountering MOD file compilation errors only with NEURON version 9.0 or later\n"
-     printf "refer to the C++ migration guide at https://nrn.readthedocs.io/en/9.0.0/guide/porting_mechanisms_to_cpp.html\n\n"
+     printf "refer to the C++ migration guide at https://www.neuronsimulator.org/en/9.0.0/guide/porting_mechanisms_to_cpp.html\n\n"
  fi
 
 exit $MAKE_STATUS

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())