Merge branch 'master' into cornu/add_eigen

neuronsimulator · Oct 12, 2023 · 6c42528 · 6c42528
2 parents efdaaa8 + 4946a24
commit 6c42528
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diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -5,6 +5,7 @@ concurrency:
   cancel-in-progress: true
 
 on:
+  merge_group:
   push:
     branches:
       - master
@@ -65,7 +66,7 @@ jobs:
           ./configure --with-python-sys-prefix --prefix=$MUSIC_INSTALL_DIR --disable-anysource
           make -j install
           deactivate
-        working-directory: ${{runner.temp}} 
+        working-directory: ${{runner.temp}}
 
       - name: Setup Xvfb
         run: |

diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -5,6 +5,7 @@ concurrency:
   cancel-in-progress: true
 
 on:
+  merge_group:
   push:
     branches:
       - master

diff --git a/.github/workflows/external.yml b/.github/workflows/external.yml
@@ -1,6 +1,6 @@
 name: External CIs
 
-concurrency: 
+concurrency:
   group: ${{ github.workflow }}#${{ github.ref }}
   cancel-in-progress: true
 
@@ -10,7 +10,7 @@ on:
 env:
   PR_URL: ${{ github.event.pull_request.html_url }}
   GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-  
+
 jobs:
   get-last-azure-url:
     runs-on: ubuntu-latest
@@ -19,7 +19,7 @@ jobs:
       azure_drop_url: ${{ steps.drop.outputs.azure_drop_url }}
       pr_azure_sha:  ${{ steps.drop.outputs.pr_azure_sha }}
     steps:
-      - id: drop 
+      - id: drop
         run: |
           # use jq to get the last Azure drop URL from the PR and the SHA1 from the same body
           export pr_json=$(gh pr view $PR_URL --json comments -q 'last(.comments[] .body | capture(".*(?<pr_azure_sha>[0-9a-f]{40}).*?(?<azure_drop_url>https://dev.azure.com/neuronsimulator/.*=zip)"))')
@@ -32,7 +32,7 @@ jobs:
           export pr_azure_sha=$(echo $pr_json | jq -r .pr_azure_sha)
           echo azure_drop_url=$azure_drop_url >> $GITHUB_OUTPUT
           echo pr_azure_sha=$pr_azure_sha >> $GITHUB_OUTPUT
-          
+
       - id: remove-label
         if: always()
         run: |
@@ -47,7 +47,7 @@ jobs:
         env:
           pr_azure_sha: ${{ steps.drop.outputs.pr_azure_sha }}
           azure_drop_url: ${{ steps.drop.outputs.azure_drop_url }}
-          
+
   nrn-modeldb-ci:
     needs: get-last-azure-url
     uses: neuronsimulator/nrn-modeldb-ci/.github/workflows/nrn-modeldb-ci.yaml@master
@@ -56,7 +56,7 @@ jobs:
       neuron_v2: neuron-nightly
 
   pr-update:
-    needs: 
+    needs:
       - nrn-modeldb-ci
       - get-last-azure-url
     runs-on: ubuntu-latest
@@ -68,4 +68,3 @@ jobs:
       env:
         ARTIFACTS_URL: ${{ github.server_url }}/${{ github.repository }}/actions/runs/${{ github.run_id }}
         pr_azure_sha: ${{ needs.get-last-azure-url.outputs.pr_azure_sha }}
-
diff --git a/.github/workflows/formatting.yml b/.github/workflows/formatting.yml
@@ -1,12 +1,13 @@
 name: Check formatting
 
-concurrency: 
+concurrency:
   group: ${{ github.workflow }}#${{ github.ref }}
-  cancel-in-progress: true  
+  cancel-in-progress: true
 
 on:
+  merge_group:
   push:
-    branches: 
+    branches:
       - release/**
   pull_request:
     branches:

diff --git a/.github/workflows/neuron-ci.yml b/.github/workflows/neuron-ci.yml
@@ -1,12 +1,13 @@
 name: NEURON CI
 
-concurrency: 
+concurrency:
   group: ${{ github.workflow }}#${{ github.ref }}
-  cancel-in-progress: true  
+  cancel-in-progress: true
 
 on:
+  merge_group:
   push:
-    branches: 
+    branches:
       # If nothing else, this is important for the ccache logic below...
       - master
       - release/**
@@ -34,7 +35,7 @@ jobs:
       SDK_ROOT: $(xcrun --sdk macosx --show-sdk-path)
       SKIP_WHEELHOUSE_REPAIR: true
       BUILD_TYPE: Release
-      DESIRED_CMAKE_VERSION: 3.15
+      DESIRED_CMAKE_VERSION: 3.17
       DYNAMIC_PYTHON_CMAKE_VERSION: 3.18
       PY_MIN_VERSION: ${{ matrix.config.python_min_version || '3.8' }}
       PY_MAX_VERSION: ${{ matrix.config.python_max_version || '3.11' }}
@@ -169,7 +170,7 @@ jobs:
           ./configure --with-python-sys-prefix --prefix=$MUSIC_INSTALL_DIR --disable-anysource
           make -j install
           deactivate
-        working-directory: ${{runner.temp}} 
+        working-directory: ${{runner.temp}}
 
       - name: Register gcc problem matcher
         if: ${{matrix.config.flag_warnings == 'ON'}}
@@ -195,7 +196,7 @@ jobs:
           repository: actions/cache
           ref: v3
           path: tmp/actions/cache
-          
+
       - name: Make actions/cache@v3 run even on failure
         run: |
           sed -i'.bak' -e '/ post-if: /d' tmp/actions/cache/action.yml

diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml
@@ -1,10 +1,11 @@
 name: Windows Installer
 
-concurrency: 
+concurrency:
   group: ${{ github.workflow }}#${{ github.ref }}
-  cancel-in-progress: true  
+  cancel-in-progress: true
 
 on:
+  merge_group:
   workflow_call:
     inputs:
       tag:
@@ -13,7 +14,7 @@ on:
         required: true
         type: string
   push:
-    branches: 
+    branches:
       - master
       - release/**
   pull_request:
@@ -54,12 +55,12 @@ jobs:
         .\nrn\ci\win_download_deps.cmd
       shell: powershell
       working-directory: ${{runner.workspace}}
-       
+
     - name: Install Dependencies
       run: .\nrn\ci\win_install_deps.cmd
       shell: powershell
       working-directory: ${{runner.workspace}}
-      
+
     - name: Build and Create Installer
       run: |
         rm.exe C:\WINDOWS\system32\bash.EXE

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -89,8 +89,6 @@ option(NRN_AVOID_ABSOLUTE_PATHS
        "Avoid embedding absolute paths in generated code (ccache optimisation)"
        ${NRN_AVOID_ABSOLUTE_PATHS_DEFAULT})
 mark_as_advanced(NRN_AVOID_ABSOLUTE_PATHS)
-option(NRN_DYNAMIC_UNITS_USE_LEGACY "Use legacy units as default for dynamic units"
-       ${NRN_DYNAMIC_UNITS_USE_LEGACY_DEFAULT})
 # note that if CoreNEURON is enabled then it is not necessary to enable this option
 option(NRN_ENABLE_MOD_COMPATIBILITY "Enable CoreNEURON compatibility for MOD files"
        ${NRN_ENABLE_MOD_COMPATIBILITY_DEFAULT})
@@ -484,6 +482,9 @@ if(NOT NRN_ENABLE_MPI_DYNAMIC OR ${num_mpi} EQUAL 1)
   set(NRN_INCLUDE_MPI_HEADERS ON)
 endif()
 
+# initialize CLI11 submodule
+cpp_cc_git_submodule(CLI11 BUILD PACKAGE CLI11 REQUIRED)
+
 # =============================================================================
 # Enable CoreNEURON support
 # =============================================================================
@@ -500,9 +501,6 @@ if(NRN_ENABLE_CORENEURON)
   set(CORENRN_ENABLE_UNIT_TESTS
       ${NRN_ENABLE_TESTS}
       CACHE BOOL "" FORCE)
-  set(CORENRN_ENABLE_LEGACY_UNITS
-      ${NRN_DYNAMIC_UNITS_USE_LEGACY}
-      CACHE BOOL "" FORCE)
   if(NRN_ENABLE_PROFILING)
     if(NRN_PROFILER STREQUAL "caliper")
       set(CORENRN_ENABLE_CALIPER_PROFILING ON)
@@ -512,9 +510,6 @@ if(NRN_ENABLE_CORENEURON)
   endif()
   set(CORENEURON_DIR ${PROJECT_SOURCE_DIR}/src/coreneuron)
 
-  # initialize CLI11 submodule
-  cpp_cc_git_submodule(CLI11 BUILD PACKAGE CLI11 REQUIRED)
-
   add_subdirectory(${PROJECT_SOURCE_DIR}/src/coreneuron)
 
   # By default `nrnivmodl` should look for `nrnivmodl-core` in the NEURON install prefix.
@@ -961,11 +956,6 @@ message(STATUS "CXX COMPILER  | ${CMAKE_CXX_COMPILER}")
 message(STATUS "BUILD_TYPE    | ${CMAKE_BUILD_TYPE} (allowed: ${allowableBuildTypes})")
 message(STATUS "COMPILE FLAGS | ${COMPILER_FLAGS}")
 message(STATUS "Shared        | ${NRN_ENABLE_SHARED}")
-if(NRN_DYNAMIC_UNITS_USE_LEGACY)
-  message(STATUS "Default units | legacy units")
-else()
-  message(STATUS "Default units | modern units (2019 nist constants)")
-endif()
 message(STATUS "MPI           | ${NRN_ENABLE_MPI}")
 if(NRN_ENABLE_MPI)
   message(STATUS "  DYNAMIC     | ${NRN_ENABLE_MPI_DYNAMIC}")
@@ -1036,9 +1026,6 @@ message(STATUS "CoreNEURON    | ${NRN_ENABLE_CORENEURON}")
 if(NRN_ENABLE_CORENEURON)
   message(STATUS "  PATH        | ${CORENEURON_DIR}")
   message(STATUS "  LINK FLAGS  | ${CORENRN_LIB_LINK_FLAGS}")
-  if(NOT coreneuron_FOUND)
-    message(STATUS "  Legacy Units| ${CORENRN_ENABLE_LEGACY_UNITS}")
-  endif()
 endif()
 if(NRN_UNIVERSAL2_BUILD)
   message(STATUS "CMAKE_OSX_ARCH| ${CMAKE_OSX_ARCHITECTURES}")

diff --git a/cmake/BuildOptionDefaults.cmake b/cmake/BuildOptionDefaults.cmake
@@ -26,7 +26,6 @@ set(NRN_ENABLE_MPI_DYNAMIC_DEFAULT OFF)
 set(NRN_ENABLE_MOD_COMPATIBILITY_DEFAULT OFF)
 set(NRN_ENABLE_REL_RPATH_DEFAULT OFF)
 set(NRN_AVOID_ABSOLUTE_PATHS_DEFAULT OFF)
-set(NRN_DYNAMIC_UNITS_USE_LEGACY_DEFAULT OFF)
 set(NRN_NMODL_CXX_FLAGS_DEFAULT "-O0")
 set(NRN_SANITIZERS_DEFAULT "")
 
@@ -68,7 +67,6 @@ set(NRN_OPTION_NAME_LIST
     NRN_MODULE_INSTALL_OPTIONS
     NRN_PYTHON_DYNAMIC
     NRN_MPI_DYNAMIC
-    NRN_DYNAMIC_UNITS_USE_LEGACY
     NRN_RX3D_OPT_LEVEL
     NRN_SANITIZERS
     CMAKE_BUILD_TYPE

diff --git a/cmake/ConfigFileSetting.cmake b/cmake/ConfigFileSetting.cmake
@@ -92,24 +92,6 @@ else()
   set(DISCRETE_EVENT_OBSERVER 0)
 endif()
 
-# No longer a user option. Default modern units. Controlled at launch by the environment variable
-# NRNUNIT_USE_LEGACY, and dynamically after launch by h.nrnunit_use_legacy(0or1). Left here solely
-# to obtain a nrnunits.lib file for modlunit. Nmodl uses the nrnunits.lib.in file.
-set(NRN_ENABLE_LEGACY_FR 0)
-if(NRN_ENABLE_LEGACY_FR)
-  set(LegacyFR 1)
-  set(LegacyY "")
-  set(LegacyN "/")
-  set(LegacyYPy "")
-  set(LegacyNPy "#")
-else()
-  set(LegacyFR 0)
-  set(LegacyY "/")
-  set(LegacyN "")
-  set(LegacyYPy "#")
-  set(LegacyNPy "")
-endif()
-
 if(NRN_ENABLE_MECH_DLL_STYLE)
   set(NRNMECH_DLL_STYLE 1)
 else()
@@ -126,12 +108,6 @@ if(NRN_ENABLE_PYTHON_DYNAMIC)
   list(APPEND NRN_COMPILE_DEFS NRNPYTHON_DYNAMICLOAD)
 endif()
 
-if(NRN_DYNAMIC_UNITS_USE_LEGACY)
-  set(DYNAMIC_UNITS_USE_LEGACY_DEFAULT 1)
-else()
-  unset(DYNAMIC_UNITS_USE_LEGACY_DEFAULT)
-endif()
-
 # =============================================================================
 # Dependencies option
 # =============================================================================
@@ -219,10 +195,8 @@ nrn_configure_file(nrnmpiuse.h src/oc)
 nrn_configure_file(nrnconfigargs.h src/nrnoc)
 nrn_configure_file(nrnneosm.h src/nrncvode)
 nrn_configure_file(sundials_config.h src/sundials)
-nrn_configure_dest_src(nrnunits.lib share/nrn/lib nrnunits.lib share/lib)
 nrn_configure_dest_src(nrn.defaults share/nrn/lib nrn.defaults share/lib)
-# NRN_DYNAMIC_UNITS requires nrnunits.lib.in be in same places as nrnunits.lib
-file(COPY ${PROJECT_SOURCE_DIR}/share/lib/nrnunits.lib.in
+file(COPY ${PROJECT_SOURCE_DIR}/share/lib/nrnunits.lib
      DESTINATION ${PROJECT_BINARY_DIR}/share/nrn/lib)
 
 if(NRN_MACOS_BUILD)
@@ -241,8 +215,6 @@ if(MINGW)
   set(nrnskip_rebase "#")
   nrn_configure_file(mknrndll.mak src/mswin/lib)
 endif()
-# TODO temporary workaround for mingw
-file(COPY ${PROJECT_BINARY_DIR}/share/nrn/lib/nrnunits.lib.in DESTINATION ${PROJECT_BINARY_DIR}/lib)
 
 # =============================================================================
 # If Interviews is not provided, configure local files

diff --git a/cmake/MacroHelper.cmake b/cmake/MacroHelper.cmake
@@ -211,11 +211,11 @@ macro(nocmodl_mod_to_cpp modfile_basename)
     OUTPUT ${PROJECT_BINARY_DIR}/${modfile_basename}.cpp
     COMMAND
       ${CMAKE_COMMAND} -E env "MODLUNIT=${PROJECT_BINARY_DIR}/share/nrn/lib/nrnunits.lib"
-      ${NRN_NOCMODL_SANITIZER_ENVIRONMENT} ${PROJECT_BINARY_DIR}/bin/nocmodl
+      ${NRN_NOCMODL_SANITIZER_ENVIRONMENT} $<TARGET_FILE:nocmodl>
       ${PROJECT_SOURCE_DIR}/${modfile_basename}.mod
     COMMAND sed "'s/_reg()/_reg_()/'" ${PROJECT_SOURCE_DIR}/${modfile_basename}.cpp >
             ${PROJECT_BINARY_DIR}/${modfile_basename}.cpp
-    COMMAND rm ${PROJECT_SOURCE_DIR}/${modfile_basename}.cpp
+    COMMAND ${CMAKE_COMMAND} -E rm ${PROJECT_SOURCE_DIR}/${modfile_basename}.cpp
     DEPENDS nocmodl ${PROJECT_SOURCE_DIR}/${modfile_basename}.mod
     WORKING_DIRECTORY ${PROJECT_BINARY_DIR}/src/nrniv)
 endmacro()

diff --git a/cmake/NeuronFileLists.cmake b/cmake/NeuronFileLists.cmake
@@ -427,7 +427,7 @@ set(NMODL_FILES_LIST
     units.cpp
     version.cpp)
 
-set(IVOS_FILES_LIST listimpl.cpp string.cpp observe.cpp regexp.cpp resource.cpp)
+set(IVOS_FILES_LIST listimpl.cpp observe.cpp regexp.cpp resource.cpp)
 
 set(MPI_DYNAMIC_INCLUDE nrnmpi_dynam.h nrnmpi_dynam_cinc nrnmpi_dynam_wrappers.inc)
 

diff --git a/cmake_nrnconf.h.in b/cmake_nrnconf.h.in
@@ -91,9 +91,6 @@
 /* Define to 1 if you have the <unistd.h> header file. */
 #undef HAVE_UNISTD_H
 
-/* 1 for legacy, undef for NIST (as of 2017), for FARADAY and R */
-#undef LegacyFR
-
 /* define if using mingw */
 #undef MINGW
 

diff --git a/docs/README.md b/docs/README.md
@@ -12,23 +12,37 @@ Contents:
 
 ### Local build
 
-#### Setup
+#### Virtual environment
 It is recommended to use a Python virtual environment, for example:
 
-```
+```bash
 python3 -m venv venv
 source venv/bin/activate
 ```
 
+
 In order to build documentation locally, you need to pip install the ``docs_requirements.txt`` :
 ```
 pip3 install -r docs/docs_requirements.txt --upgrade
 ```
 
 Also, make sure to have `Doxygen` and `pandoc` installed, and the dependencies listed in [conda_environment.yml](conda_environment.yml)
-Note that this file is tailored to the ReadTheDocs setup, but lists all desired requirements.
+Note that this conda environment file is tailored to the online ReadTheDocs setup (but it lists out all desired requirements, so make sure to check it out).
+
+#### Anaconda environment
+
+After installing Anaconda, create a new environment with the following command:
+
+```bash
+conda env create --quiet --name rtd --file docs/conda_environment.yml
+conda activate rtd
+```
+
+This will install all dependencies needed to build the documentation locally, in a similar way as on ReadTheDocs. However ReadTheDocs has a different setup, so it is of interest to head over and check the build logs for additional information.
+
+#### Confguring the build
 
-With all dependencies installed, configure project with CMake as described in [CMake Build Options](./cmake_doc/options.rst#nrn-enable-docs-bool-off).
+With all dependencies installed, configure project with CMake (>= v3.17) as described in [CMake Build Options](./cmake_doc/options.rst#nrn-enable-docs-bool-off).
 
 e.g. in your CMake build folder: