Merge branch 'master' into attempted-defenestration-of-nmodl-home

.github/workflows/nmodl-ci.yml

@@ -30,11 +30,14 @@ jobs:
               os: ubuntu-20.04
           - config:
               flag_warnings: ON
+              glibc_asserts: ON
               os: ubuntu-22.04
           - config:
               os: macos-12
           - config:
               os: macos-13
+          - config:
+              os: windows-latest
           # TODO: might be interesting to add the thread sanitizer too
           - config:
               os: ubuntu-22.04
@@ -82,6 +85,15 @@ jobs:
           echo CMAKE_BUILD_PARALLEL_LEVEL=2 >> $GITHUB_ENV
         shell: bash
 
+      - name: Install choco packages
+        if: startsWith(matrix.config.os, 'windows')
+        run: |
+          choco install winflexbison3
+
+      - name: Configure VS Toolchain (Windows)
+        if: startsWith(matrix.config.os, 'windows')
+        uses: ilammy/msvc-dev-cmd@v1
+
       - name: Set up Python3
         uses: actions/setup-python@v5
         with:
@@ -108,12 +120,17 @@ jobs:
         if: ${{matrix.config.sanitizer}}
         run: echo "::add-matcher::.github/problem-matchers/${{matrix.config.sanitizer}}.json"
 
-      - name: Configure
+      - name: Configure Windows
+        if: startsWith(matrix.config.os, 'windows')
+        run: |
+          cmake -S . -B build -DFLEX_INCLUDE_PATH=C:/ProgramData/chocolatey/lib/winflexbison3/tools -DBUILD_SHARED_LIBS=OFF
+
+      - name: Configure Linux/MacOS
+        if: ${{ !startsWith(matrix.config.os, 'windows') }}
         shell: bash
         working-directory: ${{runner.workspace}}/nmodl
         run:  |
           echo "------- Configure -------"
-          mkdir build && pushd build
           cmake_args=(-G Ninja
                       -DPYTHON_EXECUTABLE=$(which python3) \
                       -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR)
@@ -134,15 +151,20 @@ jobs:
             CXX=$(command -v clang++-14)
           else
             CXX=${CXX:-g++}
+            if [[ -n "${{matrix.config.glibc_asserts}}" ]]; then
+              cmake_args+=(-DCMAKE_BUILD_TYPE=Debug \
+                           -DCMAKE_CXX_FLAGS=-D_GLIBCXX_DEBUG)
+            fi
           fi
           cmake_args+=(-DCMAKE_CXX_COMPILER=${CXX} \
                        -DCMAKE_CXX_COMPILER_LAUNCHER=ccache)
           cmake_args+=(-DNMODL_ENABLE_BACKWARD=On)
-          cmake .. "${cmake_args[@]}"
+          cmake -B build -S . "${cmake_args[@]}"
         env:
           INSTALL_DIR: ${{ runner.workspace }}/install
 
       - name: Dump config dictionary
+        if: ${{ !startsWith(matrix.config.os, 'windows') }}
         run: |
           cat << EOF > matrix.json
           ${{toJSON(matrix.config)}}
@@ -152,6 +174,7 @@ jobs:
           echo -----
 
       - name: Restore compiler cache
+        if: ${{ !startsWith(matrix.config.os, 'windows') }}
         uses: actions/cache@v4
         with:
           path: |
@@ -162,9 +185,15 @@ jobs:
             ${{hashfiles('matrix.json')}}-
           save-always: true
 
-      - name: Build
+      - name: Build Windows
+        if: startsWith(matrix.config.os, 'windows')
+        run: |
+          cmake --build build
+  
+      - name: Build Linux/MacOS
+        if: ${{ !startsWith(matrix.config.os, 'windows') }}
         shell: bash
-        working-directory: ${{runner.workspace}}/nmodl/build
+        working-directory: ${{runner.workspace}}/nmodl
         env:
           CCACHE_BASEDIR: ${{runner.workspace}}/nmodl
           CCACHE_DIR: ${{runner.workspace}}/ccache
@@ -180,7 +209,7 @@ jobs:
           ccache -z
           # Older versions don't support -v (verbose)
           ccache -vs 2>/dev/null || ccache -s
-          cmake --build .
+          cmake --build build
           ccache -vs 2>/dev/null || ccache -s
       - name: Test
         shell: bash
@@ -191,9 +220,9 @@ jobs:
           ctest --output-on-failure -T Test
       - name: Install
         shell: bash
-        working-directory: ${{runner.workspace}}/nmodl/build
+        working-directory: ${{runner.workspace}}/nmodl
         run:  |
-          cmake --build . --target install
+          cmake --install build
 
       - name: Update references
         if: matrix.config.update_references == 'On'

.gitmodules

@@ -25,3 +25,6 @@
 [submodule "ext/backward"]
 	path = ext/backward
 	url = https://github.com/bombela/backward-cpp.git
+[submodule "ext/dlfcn-win32"]
+	path = ext/dlfcn-win32
+	url = https://github.com/dlfcn-win32/dlfcn-win32

CMakeLists.txt

@@ -130,6 +130,11 @@ if(NOT NMODL_3RDPARTY_USE_FMT
 endif()
 cpp_cc_git_submodule(json BUILD PACKAGE nlohmann_json REQUIRED)
 cpp_cc_git_submodule(pybind11 BUILD PACKAGE pybind11 REQUIRED)
+if(WIN32)
+  cpp_cc_git_submodule(dlfcn-win32 BUILD)
+  add_library(dlfcn-win32::dl ALIAS dl)
+  set(CMAKE_DL_LIBS dlfcn-win32::dl)
+endif()
 # Tell spdlog not to use its bundled fmt, it should either use the fmt submodule or a truly external
 # installation for consistency. This line should be harmless if we use an external spdlog.
 option(SPDLOG_FMT_EXTERNAL "Force to use an external {{fmt}}" ON)

azure-pipelines.yml

@@ -148,7 +148,7 @@ stages:
       submodules: True
     - script: |
         brew install flex bison cmake python@3
-        python3 -m pip install --upgrade pip setuptools
+        python3 -m pip install --upgrade pip "setuptools<=70.3.0"
         python3 -m pip install --user -r requirements.txt
       displayName: 'Install Dependencies'
     - script: |

cmake/FlexHelper.cmake

@@ -6,8 +6,10 @@
 get_filename_component(FLEX_BIN_DIR ${FLEX_EXECUTABLE} DIRECTORY)
 
 if(NOT FLEX_BIN_DIR MATCHES "/usr/bin")
-  get_filename_component(FLEX_INCLUDE_PATH ${FLEX_BIN_DIR} PATH)
-  set(FLEX_INCLUDE_PATH ${FLEX_INCLUDE_PATH}/include/)
+  if(NOT FLEX_INCLUDE_PATH)
+    get_filename_component(FLEX_INCLUDE_PATH ${FLEX_BIN_DIR} PATH)
+    set(FLEX_INCLUDE_PATH ${FLEX_INCLUDE_PATH}/include/)
+  endif()
   if(EXISTS "${FLEX_INCLUDE_PATH}/FlexLexer.h")
     message(STATUS " Adding Flex include path as : ${FLEX_INCLUDE_PATH}")
     include_directories(${FLEX_INCLUDE_PATH})

docs/contents/globals.rst

@@ -5,6 +5,7 @@ The following global variables exist:
 
   * ``GLOBAL`` visible from HOC/Python.
   * ``LOCAL`` at file scope, called top-locals.
+  * ``CONSTANT`` not visible from HOC/Python.
 
 GLOBAL variables
 ================
@@ -175,6 +176,46 @@ Collection of slightly surprising behaviour:
     the code ``nocmodl`` produces will cause a SEGFAULT.
 
 
+PARAMETER variables
+===================
+
+These can be either RANGE or not RANGE. They can be both read and write. If
+they're written to, they're converted to thread-variables. Therefore, the rest
+of this section will only describe read-only PARAMETERs.
+
+Additionally, parameters optionally have: a) a default value, b) units and c) a
+valid range.
+
+Default Values
+~~~~~~~~~~~~~~
+This section only applies to read-only PARAMETERs.
+
+The behaviour differs for RANGE variables and non-RANGE variables. For RANGE
+variables, default values need to be registered with NEURON for all PARAMETERs
+that are RANGE variables. The function is called ``hoc_register_parm_default``.
+
+Note, that NOCMODL uses it in the ``nrn_alloc`` in the generated `.cpp` files
+and also in ``ndatclas.cpp``. Therefore, it seems registering the values isn't
+optional.
+
+Non-RANGE variables are semantically equivalent to ``static double``. They're
+simply assigned their value in the definition of the global variable.
+
+CONSTANT variables
+==================
+
+These are comparatively simple. In NOCMODL they're implemented as non-const
+static doubles. They're not accessible from HOC/Python (which makes them
+simple).
+
+Quirks
+~~~~~~
+
+In certain versions of NOCMODL around `9.0` and before (and NMODL) it's
+possible to change the value of CONSTANT variables. The MOD file will still be
+considered "thread-safe" (even if it might not be).
+
+
 What Does CoreNEURON support?
 =============================
 CoreNEURON only supports read-only GLOBAL variables. Anything else needs to be

pyproject.toml

@@ -74,3 +74,6 @@ environment = { PATH = "/nmodlwheel/flex/bin:/nmodlwheel/bison/bin:$PATH" }
 # the Linux wheel is not tested in cibuildwheel due to manylinux images not having
 # libpython*.so, so this is tested manually in the CI
 test-command = "true"
+
+[tool.cibuildwheel.windows]
+environment = { SKBUILD_CMAKE_ARGS = "-DNMODL_BUILD_WHEEL=ON;-DFLEX_INCLUDE_PATH=C:/ProgramData/chocolatey/lib/winflexbison3/tools" }

src/codegen/codegen_coreneuron_cpp_visitor.cpp

@@ -66,26 +66,12 @@ std::string CodegenCoreneuronCppVisitor::simulator_name() {
 
 
 int CodegenCoreneuronCppVisitor::position_of_float_var(const std::string& name) const {
-    int index = 0;
-    for (const auto& var: codegen_float_variables) {
-        if (var->get_name() == name) {
-            return index;
-        }
-        index += var->get_length();
-    }
-    throw std::logic_error(name + " variable not found");
+    return get_prefixsum_from_name(codegen_float_variables, name);
 }
 
 
 int CodegenCoreneuronCppVisitor::position_of_int_var(const std::string& name) const {
-    int index = 0;
-    for (const auto& var: codegen_int_variables) {
-        if (var.symbol->get_name() == name) {
-            return index;
-        }
-        index += var.symbol->get_length();
-    }
-    throw std::logic_error(name + " variable not found");
+    return get_prefixsum_from_name(codegen_int_variables, name);
 }
 
 
@@ -418,7 +404,7 @@ void CodegenCoreneuronCppVisitor::print_check_table_thread_function() {
     printer->add_line("double v = 0;");
 
     for (const auto& function: info.functions_with_table) {
-        auto method_name_str = method_name(table_function_prefix() + function->get_node_name());
+        auto method_name_str = table_update_function_name(function->get_node_name());
         auto arguments = internal_method_arguments();
         printer->fmt_line("{}({});", method_name_str, arguments);
     }

src/codegen/codegen_cpp_visitor.cpp

@@ -72,8 +72,8 @@ bool CodegenCppVisitor::has_parameter_of_name(const T& node, const std::string&
 }
 
 
-std::string CodegenCppVisitor::table_function_prefix() const {
-    return "lazy_update_";
+std::string CodegenCppVisitor::table_update_function_name(const std::string& block_name) const {
+    return "update_table_" + method_name(block_name);
 }
 
 
@@ -404,17 +404,7 @@ std::pair<std::string, std::string> CodegenCppVisitor::write_ion_variable_name(
 
 
 int CodegenCppVisitor::get_int_variable_index(const std::string& var_name) {
-    auto it = std::find_if(codegen_int_variables.cbegin(),
-                           codegen_int_variables.cend(),
-                           [&var_name](const auto& int_var) {
-                               return int_var.symbol->get_name() == var_name;
-                           });
-
-    if (it == codegen_int_variables.cend()) {
-        throw std::runtime_error(fmt::format("Unknown int variable: {}", var_name));
-    }
-
-    return static_cast<int>(it - codegen_int_variables.cbegin());
+    return get_index_from_name(codegen_int_variables, var_name);
 }
 
 
@@ -473,9 +463,7 @@ void CodegenCppVisitor::print_function_call(const FunctionCall& node) {
         }
         return {name, false};
     };
-    std::string function_name;
-    bool is_random_function;
-    std::tie(function_name, is_random_function) = get_renamed_random_function(name);
+    auto [function_name, is_random_function] = get_renamed_random_function(name);
 
     if (defined_method(name)) {
         function_name = method_name(name);
@@ -1353,7 +1341,7 @@ void CodegenCppVisitor::setup(const Program& node) {
     info.mod_file = mod_filename;
 
     if (info.mod_suffix == "") {
-        info.mod_suffix = std::filesystem::path(mod_filename).stem();
+        info.mod_suffix = std::filesystem::path(mod_filename).stem().string();
     }
     info.rsuffix = info.point_process ? "" : "_" + info.mod_suffix;
 
@@ -1524,9 +1512,8 @@ void CodegenCppVisitor::print_table_check_function(const Block& node) {
     auto float_type = default_float_data_type();
 
     printer->add_newline(2);
-    printer->fmt_push_block("void {}{}({})",
-                            table_function_prefix(),
-                            method_name(name),
+    printer->fmt_push_block("void {}({})",
+                            table_update_function_name(name),
                             get_parameter_str(internal_params));
     {
         printer->fmt_push_block("if ({} == 0)", use_table_var);

src/codegen/codegen_cpp_visitor.hpp

@@ -169,6 +169,47 @@ struct ShadowUseStatement {
     std::string rhs;
 };
 
+inline std::string get_name(const std::shared_ptr<symtab::Symbol>& sym) {
+    return sym->get_name();
+}
+
+inline std::string get_name(const IndexVariableInfo& var) {
+    return var.symbol->get_name();
+}
+
+template <class T>
+int get_index_from_name(const std::vector<T>& variables, const std::string& name) {
+    auto it = std::find_if(variables.cbegin(), variables.cend(), [&name](const auto& var) {
+        return get_name(var) == name;
+    });
+
+    if (it == variables.cend()) {
+        throw std::runtime_error(fmt::format("Unknown variable: {}", name));
+    }
+
+    return static_cast<int>(it - variables.cbegin());
+}
+
+inline int get_length(const std::shared_ptr<symtab::Symbol>& sym) {
+    return sym->get_length();
+}
+
+inline int get_length(const IndexVariableInfo& var) {
+    return var.symbol->get_length();
+}
+
+template <class T>
+int get_prefixsum_from_name(const std::vector<T>& variables, const std::string& name) {
+    int index = 0;
+    for (const auto& var: variables) {
+        if (get_name(var) == name) {
+            return index;
+        }
+        index += get_length(var);
+    }
+    throw std::logic_error(name + " variable not found");
+}
+
 /** \} */  // end of codegen_details
 
 
@@ -1112,10 +1153,12 @@ class CodegenCppVisitor: public visitor::ConstAstVisitor {
                                           bool use_instance = true) const = 0;
 
     /**
-     * Prefix used for the function that performs the lazy update
+     * The name of the function that updates the table value if the parameters
+     * changed.
+     *
+     * \param block_name  The name of the block that contains the TABLE.
      */
-    std::string table_function_prefix() const;
-
+    std::string table_update_function_name(const std::string& block_name) const;
 
     /**
      * Return ion variable name and corresponding ion read variable name.