Merge branch 'master' into arith_object_flux

.github/workflows/coverage.yml

@@ -73,7 +73,7 @@ jobs:
           sudo apt-get install xvfb
           sudo /usr/bin/Xvfb $DISPLAY -screen 0 1600x1200x24 -noreset -nolock -shmem &  # run in bg
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 2
 
@@ -83,7 +83,7 @@ jobs:
             git submodule update --init --recursive --force --depth 1 -- external/nmodl
 
       - name: Set up Python@${{ env.PY_MIN_VERSION }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ env.PY_MIN_VERSION }}
 
@@ -95,12 +95,12 @@ jobs:
           python -m pip install --upgrade -r ci_requirements.txt
 
       - name: Set up Python@${{ env.PY_MID_VERSION }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ env.PY_MID_VERSION }}
 
       - name: Set up Python@${{ env.PY_MAX_VERSION }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ env.PY_MAX_VERSION }}
 
@@ -184,7 +184,7 @@ jobs:
         if: failure() && contains(github.event.pull_request.title, 'live-debug-coverage')
         uses: mxschmitt/action-tmate@v3
 
-      - uses: codecov/codecov-action@v3
+      - uses: codecov/codecov-action@v4
         with:
           directory: ./build
           fail_ci_if_error: true

.github/workflows/docs.yml

@@ -36,11 +36,11 @@ jobs:
         shell: bash
 
       - name: Set up Python@${{ env.DEFAULT_PY_VERSION }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ env.DEFAULT_PY_VERSION }}
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Install Python dependencies
         working-directory: ${{runner.workspace}}/nrn

.github/workflows/formatting.yml

@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-22.04
     timeout-minutes: 5
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Update submodule
         working-directory: ${{runner.workspace}}/nrn
         run: git submodule update --init external/coding-conventions

.github/workflows/neuron-ci.yml

@@ -127,7 +127,7 @@ jobs:
           echo CI_OS_NAME=linux >> $GITHUB_ENV
         shell: bash
 
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           fetch-depth: 2
 
@@ -138,7 +138,7 @@ jobs:
 
       - name: Set up Python@${{ env.PY_MIN_VERSION }}
         if: ${{matrix.config.python_dynamic == 'ON'}}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ env.PY_MIN_VERSION }}
 
@@ -151,7 +151,7 @@ jobs:
           python -m pip install --upgrade -r ci_requirements.txt
 
       - name: Set up Python@${{ env.PY_MAX_VERSION }}
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: ${{ env.PY_MAX_VERSION }}
 
@@ -198,7 +198,7 @@ jobs:
 
       # Workaround for https://github.com/actions/cache/issues/92
       - name: Checkout cache action
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           repository: actions/cache
           ref: v3

.github/workflows/release.yml

@@ -25,7 +25,7 @@ jobs:
       release_url: ${{ steps.create_release.outputs.upload_url }}
       rel_tag: ${{ env.REL_TAG }}
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         name: Checkout branch ${{ env.REL_BRANCH }}
         with:
             ref: ${{ env.REL_BRANCH }}

.github/workflows/windows.yml

@@ -35,7 +35,7 @@ jobs:
     timeout-minutes: 45
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
       with:
         ref: ${{ inputs.tag }}
 
@@ -46,7 +46,7 @@ jobs:
       working-directory: ${{runner.workspace}}\nrn
 
     - name: Set up Python3
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: '3.11'
 
@@ -79,7 +79,7 @@ jobs:
       uses: mxschmitt/action-tmate@v3
 
     - name: Upload build artifact
-      uses: actions/upload-artifact@v3
+      uses: actions/upload-artifact@v4
       with:
         name: nrn-nightly-AMD64.exe
         path: ${{runner.workspace}}\nrn\nrn-nightly-AMD64.exe

.gitlab-ci.yml

@@ -7,7 +7,6 @@ include:
   - project: hpc/gitlab-upload-logs
     file: enable-upload.yml
 
-
 # see https://gitlab.com/gitlab-org/gitlab/-/issues/263401 for why we specify the flags like this now
 # 130 characters seems to be the point at which jobs refuse to run
 .matrix:
@@ -263,3 +262,60 @@ test:neuron:nmodl:nvhpc:omp:legacy:
 test:neuron:nmodl:nvhpc:omp:
   extends: [.test_neuron, .gpu_node]
   needs: ["build:neuron:nmodl:nvhpc:omp"]
+
+
+# Container building
+mac_m1_container_build:
+  stage: .pre
+  tags:
+    - macos-arm64
+  script:
+    - if [ -z "${ARM64_IMAGE_TAG}" ]; then
+    -   echo "Please set the ARM64_IMAGE_TAG variable"
+    -   exit 1
+    - fi
+    - cd packaging/python
+    - echo "Replacing symlinks with their targets to keep podman happy"
+    - find . -type l -exec cp $(realpath {}) ./TEMP \; -exec rm {} \; -exec mv TEMP {} \;
+    - ls -l
+    - export BUILDAH_FORMAT=docker # enables ONBUILD instructions which are not OCI compatible
+    - machine_status=$(podman machine inspect | awk '/State/ {print $2}' | tr -d '",')
+      # If you start the machine yourself, make sure BUILDAH_FORMAT and the http proxy variables are set in the shell before doing so!
+    - if [[ "${machine_status}" != "running" ]]; then
+    -     echo "Machine is in ${machine_status} status - starting"
+    -     podman machine start
+    - fi
+    - podman build -t neuronsimulator/neuron_wheel:${ARM64_IMAGE_TAG} --build-arg MANYLINUX_IMAGE=manylinux2014_aarch64 -f Dockerfile .
+    - podman login -u ${DOCKER_HUB_USER} -p ${DOCKER_HUB_AUTH_TOKEN} docker.io
+    - podman push neuronsimulator/neuron_wheel:${ARM64_IMAGE_TAG}
+    - podman rmi localhost/neuronsimulator/neuron_wheel:${ARM64_IMAGE_TAG}
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "web"
+  when: manual
+
+x86_64_container_build:
+  stage: .pre
+  image:
+    name: quay.io/buildah/stable
+    entrypoint: [""]
+  variables:
+    KUBERNETES_CPU_LIMIT: 4
+    KUBERNETES_CPU_REQUEST: 2
+    KUBERNETES_MEMORY_LIMIT: 8Gi
+    KUBERNETES_MEMORY_REQUEST: 4Gi
+  tags:
+    - kubernetes
+  rules:
+    - if: $CI_PIPELINE_SOURCE == "web"
+  when: manual
+  script:
+    - if [ -z "${X86_IMAGE_TAG}" ]; then
+    -   echo "Please set the X86_IMAGE_TAG variable"
+    -   exit 1
+    - fi
+    - export STORAGE_DRIVER=vfs    # allows to build inside containers without additional mounts
+    - export BUILDAH_FORMAT=docker # enables ONBUILD instructions which are not OCI compatible
+    - cd packaging/python
+    - buildah bud --iidfile image_id -t neuronsimulator/neuron_wheel:${X86_IMAGE_TAG} -f Dockerfile .
+    - buildah login -u ${DOCKER_HUB_USER} -p ${DOCKER_HUB_AUTH_TOKEN} docker.io
+    - buildah push $(<image_id) docker://docker.io/neuronsimulator/neuron_wheel:${X86_IMAGE_TAG}

.readthedocs.yml

@@ -1,4 +1,9 @@
 version: 2
 
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "mambaforge-22.9"
+
 conda:
   environment: docs/conda_environment.yml

CMakeLists.txt

@@ -827,10 +827,11 @@ if(NRN_ENABLE_TESTS)
       "${neurondemo_prefix}/${CMAKE_SHARED_LIBRARY_PREFIX}nrnmech${CMAKE_SHARED_LIBRARY_SUFFIX}")
   add_custom_command(
     OUTPUT ${neurondemo_files}
-    COMMAND
-      ${CMAKE_COMMAND} -E env ${NRN_RUN_FROM_BUILD_DIR_ENV} ${NRN_SANITIZER_ENABLE_ENVIRONMENT}
-      "${PROJECT_BINARY_DIR}/bin/neurondemo" "-nobanner" "-nogui" "-c" "quit()"
+    COMMAND ${CMAKE_COMMAND} -E env ${NRN_RUN_FROM_BUILD_DIR_ENV}
+            ${NRN_SANITIZER_ENABLE_ENVIRONMENT} "${PROJECT_BINARY_DIR}/bin/nrnivmodl"
+    WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/share/nrn/demo/release
     VERBATIM)
+
   add_custom_target(generate-neurondemo-mechanism-library ALL DEPENDS ${neurondemo_files} nrniv
                                                                       copy_share_lib_to_build)
   # Initialize the submodule *before* including the test/CMakeLists.txt that uses it. This ensures

cmake/CMakeListsNrnMech.cmake

@@ -23,48 +23,60 @@ endif()
 # Interview might have linked to libnrniv but we don't want to link to special
 list(REMOVE_ITEM NRN_LINK_LIBS "interviews")
 
-# CMake does some magic to transform sys libs to -l<libname>. We replicate it
-foreach(link_lib ${NRN_LINK_LIBS})
-  # skip static readline library as it will be linked to nrniv (e.g. with wheel) also stub libraries
-  # from OSX can be skipped
-  if("${link_lib}" MATCHES "(libreadline.a|/*.tbd)")
-    continue()
-  endif()
+function(get_link_libraries libs)
+  # CMake does some magic to transform sys libs to -l<libname>. We replicate it
+  foreach(link_lib ${libs})
+    # skip static readline library as it will be linked to nrniv (e.g. with wheel) also stub
+    # libraries from OSX can be skipped
+    if("${link_lib}" MATCHES "(libreadline.a|/*.tbd)")
+      continue()
+    endif()
 
-  get_filename_component(dir_path ${link_lib} DIRECTORY)
-  if(TARGET ${link_lib})
-    get_property(
-      link_flag
-      TARGET ${link_lib}
-      PROPERTY INTERFACE_LINK_LIBRARIES)
-    set(description
-        "Extracting link flags from target '${link_lib}', beware that this can be fragile.")
-    # Not use it yet because it can be generator expressions get_property(compile_flag TARGET
-    # ${link_lib} PROPERTY INTERFACE_COMPILE_OPTIONS) string(APPEND NRN_COMPILE_DEFS
-    # ${compile_flag})
-  elseif(NOT dir_path)
-    set(link_flag "-l${link_lib}")
-    set(description
-        "Generating link flags from name '${link_lib}', beware that this can be fragile.")
-    # avoid library paths from special directory /nrnwheel which used to build wheels under docker
-    # container
-  elseif("${dir_path}" MATCHES "^/nrnwheel")
-    continue()
-  elseif("${dir_path}" MATCHES "^(/lib|/lib64|/usr/lib|/usr/lib64)$")
-    # NAME_WLE not avaialble with CMake version < 3.14
-    get_filename_component(libname ${link_lib} NAME)
-    string(REGEX REPLACE "\\.[^.]*$" "" libname_wle ${libname})
-    string(REGEX REPLACE "^lib" "" libname_wle ${libname_wle})
-    set(link_flag "-l${libname_wle}")
-    set(description
-        "Extracting link flags from path '${link_lib}', beware that this can be fragile.")
-  else()
-    set(link_flag "${link_lib} -Wl,-rpath,${dir_path}")
-    set(description "Generating link flags from path ${link_lib}")
-  endif()
-  message(NOTICE "${description} Got: ${link_flag}")
-  string(APPEND NRN_LINK_DEFS " ${link_flag}")
-endforeach()
+    get_filename_component(dir_path ${link_lib} DIRECTORY)
+    if(TARGET ${link_lib})
+      get_property(
+        sublink_flag
+        TARGET ${link_lib}
+        PROPERTY INTERFACE_LINK_LIBRARIES)
+      set(description
+          "Extracting link flags from target '${link_lib}', beware that this can be fragile.")
+      # Not use it yet because it can be generator expressions get_property(compile_flag TARGET
+      # ${link_lib} PROPERTY INTERFACE_COMPILE_OPTIONS) string(APPEND NRN_COMPILE_DEFS
+      # ${compile_flag})
+      foreach(sublink_lib ${sublink_flag})
+        if(TARGET ${sublink_lib})
+          message(NOTICE "For '${link_lib}' going to see TARGET '${sublink_lib}' recursively.")
+          get_link_libraries(${sublink_lib})
+        else()
+          set(link_flag "${link_flag} ${sublink_flag}")
+        endif()
+      endforeach()
+    elseif(NOT dir_path)
+      set(link_flag "-l${link_lib}")
+      set(description
+          "Generating link flags from name '${link_lib}', beware that this can be fragile.")
+      # avoid library paths from special directory /nrnwheel which used to build wheels under docker
+      # container
+    elseif("${dir_path}" MATCHES "^/nrnwheel")
+      continue()
+    elseif("${dir_path}" MATCHES "^(/lib|/lib64|/usr/lib|/usr/lib64)$")
+      # NAME_WLE not avaialble with CMake version < 3.14
+      get_filename_component(libname ${link_lib} NAME)
+      string(REGEX REPLACE "\\.[^.]*$" "" libname_wle ${libname})
+      string(REGEX REPLACE "^lib" "" libname_wle ${libname_wle})
+      set(link_flag "-l${libname_wle}")
+      set(description
+          "Extracting link flags from path '${link_lib}', beware that this can be fragile.")
+    else()
+      set(link_flag "${link_lib} -Wl,-rpath,${dir_path}")
+      set(description "Generating link flags from path ${link_lib}")
+    endif()
+    message(NOTICE "${description} Got: ${link_flag}")
+    string(APPEND NRN_LINK_DEFS " ${link_flag}")
+  endforeach()
+endfunction(get_link_libraries)
+
+get_link_libraries("${NRN_LINK_LIBS}")
 
 # Compiler flags depending on cmake build type from BUILD_TYPE_<LANG>_FLAGS
 string(TOUPPER "${CMAKE_BUILD_TYPE}" _BUILD_TYPE)

cmake/CompilerHelper.cmake

@@ -51,7 +51,7 @@ if(CMAKE_C_COMPILER_ID MATCHES "PGI" OR CMAKE_C_COMPILER_ID MATCHES "NVHPC")
     # Random123 does not play nicely with NVHPC 21.11+'s detection of ABM features, see:
     # https://github.com/BlueBrain/CoreNeuron/issues/724 and
     # https://github.com/DEShawResearch/random123/issues/6.
-    list(APPEND NRN_COMPILE_DEFS R123_USE_INTRIN_H=0)
+    list(APPEND NRN_R123_COMPILE_DEFS R123_USE_INTRIN_H=0)
   endif()
 else()
   set(NRN_HAVE_NVHPC_COMPILER OFF)