Merge branch '1uc/update-clang-format' of github.com:BlueBrain/nmodl …

…into 1uc/update-clang-format

.github/workflows/nmodl-ci.yml

@@ -15,7 +15,7 @@ on:
       - release/**
 
 env:
-  PYTHON_VERSION: 3.8
+  PYTHON_VERSION: 3.9
   DESIRED_CMAKE_VERSION: 3.15.0
 
 jobs:

.github/workflows/nmodl-doc.yml

@@ -16,7 +16,7 @@ on:
 
 env:
   BUILD_TYPE: Release
-  PYTHON_VERSION: 3.8
+  PYTHON_VERSION: 3.9
   DESIRED_CMAKE_VERSION: 3.15.0
 
 jobs:

CMakeLists.txt

@@ -177,7 +177,7 @@ endif()
 # Find required python packages
 # =============================================================================
 message(STATUS "CHECKING FOR PYTHON")
-find_package(Python 3.8 REQUIRED COMPONENTS Interpreter)
+find_package(Python 3.9 REQUIRED COMPONENTS Interpreter)
 cpp_cc_strip_python_shims(EXECUTABLE "${PYTHON_EXECUTABLE}" OUTPUT PYTHON_EXECUTABLE)
 
 # =============================================================================

INSTALL.rst

@@ -30,7 +30,7 @@ support is necessary. Make sure you have following packages available:
 -  flex (>=2.6)
 -  bison (>=3.0)
 -  CMake (>=3.15)
--  Python (>=3.8)
+-  Python (>=3.9)
 -  Python packages : jinja2 (>=2.10), pyyaml (>=3.13), pytest (>=4.0.0),
    sympy (>=1.3), textwrap
 

azure-pipelines.yml

@@ -84,10 +84,10 @@ stages:
         sudo apt-add-repository -y ppa:deadsnakes/ppa
         sudo apt-get update
         sudo apt-get install -y g++-9 flex bison libfl-dev cython libx11-dev libxcomposite-dev libncurses-dev mpich
-        sudo apt-get install -y python3.8 python3.8-dev python3.8-venv ninja-build
+        sudo apt-get install -y python3.9 python3.9-dev python3.9-venv ninja-build
         sudo apt-get remove -y python3-importlib-metadata
-        python3.8 -m pip install --upgrade pip setuptools
-        python3.8 -m pip install --user -r requirements.txt
+        python3.9 -m pip install --upgrade pip setuptools
+        python3.9 -m pip install --user -r requirements.txt
         # we manually get version 3.15.0 to make sure that changes in the cmake
         # files do not require unsupported versions of cmake in our package.
         wget --quiet --output-document=- "https://github.com/Kitware/CMake/releases/download/$CMAKE_VER/$CMAKE_PKG.tar.gz" | tar xzpf -
@@ -101,7 +101,7 @@ stages:
         mkdir -p $(Build.Repository.LocalPath)/build
         cd $(Build.Repository.LocalPath)/build
         cmake --version
-        cmake .. -DPYTHON_EXECUTABLE=$(which python3.8) -DCMAKE_INSTALL_PREFIX=$HOME/nmodl -DCMAKE_BUILD_TYPE=Release
+        cmake .. -DPYTHON_EXECUTABLE=$(which python3.9) -DCMAKE_INSTALL_PREFIX=$HOME/nmodl -DCMAKE_BUILD_TYPE=Release
         make -j 2
         if [ $? -ne 0 ]
         then
@@ -121,7 +121,7 @@ stages:
         mkdir nrn/build
         cd nrn/build
         cmake --version
-        cmake .. -DNRN_ENABLE_CORENEURON=ON -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_RX3D=OFF -DNRN_ENABLE_MPI=ON -DNRN_ENABLE_TESTS=ON -DCORENRN_ENABLE_NMODL=ON -DCORENRN_NMODL_DIR=$HOME/nmodl -DPYTHON_EXECUTABLE=$(which python3.8) -DCORENRN_NMODL_FLAGS="sympy --analytic"
+        cmake .. -DNRN_ENABLE_CORENEURON=ON -DNRN_ENABLE_INTERVIEWS=OFF -DNRN_ENABLE_RX3D=OFF -DNRN_ENABLE_MPI=ON -DNRN_ENABLE_TESTS=ON -DCORENRN_ENABLE_NMODL=ON -DCORENRN_NMODL_DIR=$HOME/nmodl -DPYTHON_EXECUTABLE=$(which python3.9) -DCORENRN_NMODL_FLAGS="sympy --analytic"
         make -j 2
         if [ $? -ne 0 ]
         then
@@ -215,7 +215,7 @@ stages:
       displayName: "Set wheel tag"
 
     - script: |
-        echo "##vso[task.setvariable variable=CIBW_BUILD;]cp38* cp312*"
+        echo "##vso[task.setvariable variable=CIBW_BUILD;]cp39* cp312*"
         echo "Build identifiers: $CIBW_BUILD"
       condition: and(succeeded(), eq(variables['Build.Reason'], 'PullRequest'))
       displayName: "Set build identifiers"
@@ -260,7 +260,7 @@ stages:
       displayName: "Set wheel tag"
 
     - script: |
-        echo "##vso[task.setvariable variable=CIBW_BUILD;]cp38* cp312*"
+        echo "##vso[task.setvariable variable=CIBW_BUILD;]cp39* cp312*"
         echo "Build identifiers: $CIBW_BUILD"
       condition: and(succeeded(), eq(variables['Build.Reason'], 'PullRequest'))
       displayName: "Set build identifiers"
@@ -291,8 +291,6 @@ stages:
     strategy:
       matrix:
         ${{ if eq(variables.buildWheel, True) }}:
-          Python38:
-            python.version: '3.8'
           Python39:
             python.version: '3.9'
           Python310:

pyproject.toml

@@ -14,7 +14,7 @@ dependencies = [
     "importlib-resources;python_version<'3.9'",
 ]
 scripts = {nmodl = "nmodl._binwrapper:main"}
-requires-python = ">=3.8"
+requires-python = ">=3.9"
 
 optional-dependencies.test = ["pytest>=3.3.0", "pytest-cov", "numpy", "scipy"]
 optional-dependencies.docs = [
@@ -76,4 +76,4 @@ environment = { PATH = "/nmodlwheel/flex/bin:/nmodlwheel/bison/bin:$PATH" }
 test-command = "true"
 
 [tool.cibuildwheel.windows]
-environment = { SKBUILD_CMAKE_ARGS = "-DNMODL_BUILD_WHEEL=ON;-DFLEX_INCLUDE_PATH=C:/ProgramData/chocolatey/lib/winflexbison3/tools" }
+environment = { SKBUILD_CMAKE_ARGS = "-DNMODL_BUILD_WHEEL=ON;-DFLEX_INCLUDE_PATH=C:/ProgramData/chocolatey/lib/winflexbison3/tools" }

src/codegen/codegen_helper_visitor.cpp

@@ -290,7 +290,7 @@ void CodegenHelperVisitor::find_non_range_variables() {
 
         // if model is thread safe and if parameter is being written then
         // those variables should be promoted to thread safe variable
-        if (info.vectorize && info.thread_safe && var->get_write_count() > 0) {
+        if (info.vectorize && info.declared_thread_safe && var->get_write_count() > 0) {
             var->mark_thread_safe();
             info.thread_variables.push_back(var);
             info.thread_var_data_size += var->get_length();

src/codegen/codegen_neuron_cpp_visitor.cpp

@@ -1103,6 +1103,7 @@ void CodegenNeuronCppVisitor::print_neuron_includes() {
     printer->add_multi_line(R"CODE(
         #include "mech_api.h"
         #include "neuron/cache/mechanism_range.hpp"
+        #include "nmodlmutex.h"
         #include "nrniv_mf.h"
         #include "section_fwd.hpp"
     )CODE");
@@ -3063,6 +3064,14 @@ void CodegenNeuronCppVisitor::visit_for_netcon(const ast::ForNetcon& node) {
     printer->pop_block();
 }
 
+void CodegenNeuronCppVisitor::visit_protect_statement(const ast::ProtectStatement& node) {
+    printer->add_line("_NMODLMUTEXLOCK");
+    printer->add_indent();
+    node.get_expression()->accept(*this);
+    printer->add_text(";");
+    printer->add_line("_NMODLMUTEXUNLOCK");
+}
+
 
 }  // namespace codegen
 }  // namespace nmodl

src/codegen/codegen_neuron_cpp_visitor.hpp

@@ -839,6 +839,7 @@ class CodegenNeuronCppVisitor: public CodegenCppVisitor {
     void visit_for_netcon(const ast::ForNetcon& node) override;
     void visit_longitudinal_diffusion_block(const ast::LongitudinalDiffusionBlock& node) override;
     void visit_lon_diffuse(const ast::LonDiffuse& node) override;
+    void visit_protect_statement(const ast::ProtectStatement& node) override;
 
   public:
     /****************************************************************************************/

test/usecases/CMakeLists.txt

@@ -25,6 +25,7 @@ set(NMODL_USECASE_DIRS
     point_process
     pointer
     procedure
+    protect
     random
     solve
     state

test/usecases/protect/shared_counter.mod

@@ -0,0 +1,17 @@
+NEURON {
+    SUFFIX shared_counter
+    GLOBAL g_cnt
+}
+
+ASSIGNED {
+    g_cnt
+}
+
+
+INITIAL {
+    PROTECT g_cnt = 0
+}
+
+BREAKPOINT {
+    PROTECT g_cnt = g_cnt + 1
+}

test/usecases/protect/test_shared_counter.py

@@ -0,0 +1,30 @@
+from neuron import h, gui
+
+
+def test_shared_counter():
+    nthreads = 32
+    nseg = 10
+    nsteps = 100
+
+    sections = [h.Section() for _ in range(nthreads)]
+    for s in sections:
+        s.insert("shared_counter")
+        s.nseg = nseg
+
+    pc = h.ParallelContext()
+
+    pc.nthread(nthreads)
+    for k, s in enumerate(sections):
+        pc.partition(k, h.SectionList([s]))
+
+    h.finitialize()
+    for _ in range(nsteps):
+        h.step()
+
+    expected = nthreads * nseg * nsteps
+    g_cnt = h.g_cnt_shared_counter
+    assert h.g_cnt_shared_counter == expected, f"{g_cnt}"
+
+
+if __name__ == "__main__":
+    test_shared_counter()